################################################################### # # This is the November 21 2022 release of the BUSTER package (BUSTER, RhoFit, # Gelly, Grade/Grade2, buster-report and Pipedream). # # This version is avaiable for all academic users. # ################################################################### # # Copyright (C) 2003-2022 by Global Phasing Limited # # All rights reserved. # # This software is proprietary to and embodies the # confidential technology of Global Phasing Limited # (GPhL). Possession, use, duplication or dissemination of # the software is authorised only pursuant to a valid # written licence from GPhL. # # Authors: G. Bricogne, E. Blanc, M. Brandl, C. Flensburg, P. Keller, # W. Paciorek, P. Roversi, A. Sharff, O. Smart, C. Vonrhein, # T. Womack # ################################################################### =================================================================== Changes since the last release Nov 21 2022 (for BUSTER, Pipedream, RhoFit and Grade/Grade2) =================================================================== ### Improvements and new features: * Added to aB_deposition_combine the capability to also work with phenix.refine or REFMAC refinement results when (1) generating a combined reflection mmCIF file from data processing (e.g. autoPROC+STARANISO PDBx/mmCIF file Data_1_autoPROC_STARANISO_all.cif) and refinement, and (2) transfering the data processing statsitics (data quality metrics) from the correct data block into the model PDBx/mmCIF file for deposition. Thanks to Luca Jovine for discussions and examples. This is work-in-progress and we would appreciate any feedback about experience with those files when depositing to the wwPDB (or using their validation server). Please note that reflection data from REFMAC need to be internally re-scaled (taking anisotropic Bij recorded in the model mmCIF file after refinement) in order to reliably compare the unmodified, original data (as input into REFMAC) to the data processing data. * Multiple items regarding the Grade2 restraints dictionary generator: * Grade2 now sets the CCP4-extension CIF item _chem_comp.group whenever possible for PDB chemical components and modified amino acids. A new command-line option --group allows _chem_comp.group to be manually set. This extension facilitates the use of Grade2 CIF restraint dictionaries in Coot. Thanks to Chip Lesburg for suggesting this extension. * A new Grade2 option --lookup ID allows an external script to be invoked to look up details of a molecule from a corporate (or public) database and then run Grade2 to produce restraints for it. The environment variable BDG_GRADE2_LIGAND_LOOKUP is used to set the location of the script to be used. Please see https://gitlab.com/gphl/grade2_lookup_scripts for example scripts written in different languages and a description of how to write your own lookup script. Thanks to Christian Schleberger for suggesting this extension. * Grade2 will now write the systematic (IUPAC) name of the ligand, if it is available, to the output CIF restraint dictionary. Systematic names for PDB ligands are automatically obtained from the input PDB chemical component definition. The --systematic option allows the systematic name to be manually set. Thanks to Gilbert Bey for suggesting this extension. * A new Grade2 option --pubchem_names can be used to search online for the systematic name of a molecule by looking for it in the PubChem Database. As the process involves uploading the SMILES string of the molecule to PubChem it should not be used for confidential ligands. For security reasons, the option is deactivated by default. * The new Grade2 option --aa_loose extends setting atom IDs to "non-standard" amino acids. By default, only alpha amino acids with an unmodified amino group are recognized. --aa_loose extends recognition to N-modified amino acids, Aib-like amino acids with two beta carbon atoms, Gly-like amino acids and beta amino acids. Thanks to Markus Rudolph for suggesting this enhancement. * When requesting certain parameter classes to be fixed or active (e.g. XYZ, OCC or B): ADP parameters will be handled together with all other (isotropic) B parameters - e.g. as part of the AlternatingRefinement macro. * The generation of occupancy-refinement instructions via the pdb2occ tool now also allows specification of the restraint sigma for occupancy sum (BUSTER_OCCSUM specification): the parameter Pdb2OccSumSigma defaults to 0.005. * The analysis of likelihood outliers has been improved via an initial analysis of (known) ice-ring resolution ranges to provide feedback and possible warnings to the user. This includes newly added very high-resolution ice-ring ranges derived from data collected by Gleb Bourenkov (EMBL-Hamburg, Petra-III/P14). * If anomalous data was provided in the input MTZ file, the output MTZ reflection file (refine.mtz) will also contain F_ano/PHI_ano columns to compute anomalous Fourier maps within Coot. The phase of the 2mFo-DFc electron density map is used here already with a phase shift of -90 degree. ### Changes: * Grade Following the release of Grade2, the successor to Grade, in July 2021, and its maturation over the past 15 months, we have decided that now is the appropriate time to bring to a close any further development and support for Grade itself, 12 years after its initial release. All further development effort will now be concentrated on Grade2. This release is therefore the final one for which Grade will remain under development and will be supported. From the next release, Grade will move to becoming an unsupported program, prior to its removal from our distribution at a date yet to be decided. We would urge users to take this opportunity to move over to using Grade2. * Several changes in the aB_autorefine tool to limit the number of individual stages (resulting in fewer refinement iterations): * Better handling of the decision regarding TLS and/or ADP refinement (avoiding doing TLS when ADP will be done later anyway). * Skipping the first water update if there are already water residues in the input PDB file - and go directly into the 2nd-shell water update (if resolution at least 2.5A). * If the input PDB already contains (only) full-occupancy hydrogens, the job dealing with hydrogen addition will be skipped. * A new command-line argument (-RIG/-noRIG) allows control of the (default) initial rigid-body refinement step. Furthermore, the statistics of that initial RB step will not be reported in the overall summary.png file by default (change parameter aB_autorefine_ReportRB to "yes" if you want to include it) - to avoid uninformative plots due to a large initial drop of e.g. R/Rfree at the very first RB step. * Added a new FAQ "Security: does Grade2 upload any ligand information to public servers?" See https://gphl.gitlab.io/grade2_docs/faqs.html#faq-security * When keeping coordinate parameters fixed, also set the weight for geometric restraints only affecting those parameters to zero. ### Fixes: * For the Grade2 restraints generator: * Fixed problem when Grade2 is supplied with a SMILES input that is then charged leading to atoms being reordered during the charging process, causing chiral inversions compared to the original input. Thanks to Andrew Sharff and Matthias Zebisch for reporting the bug. * Grade2 can now read SD files produced by MOE whose terminating line M END lacks the M character. Thanks to Markus Rudolph for raising this issue. * The SVG schematic 2D molecular diagrams have been improved to remove misleading wedge indications of chirality from non-carbon atoms. * A number of other small improvements and fixes to Grade2 have been made, as listed in the Changelog: https://gphl.gitlab.io/grade2_docs/changelog.html =================================================================== = Release 8th June 2022 =================================================================== ### Fixes: * Update to the release of 3rd June 2022, correcting the accidental omission of aB_autorefine. =================================================================== = Release 3rd June 2022 =================================================================== ### Improvements and new features: * Grade2 will now (by default) recognize an alpha amino acid when supplied with an input that lacks atom IDs (aka atom names) for instance a SMILES string. If an alpha amino acid is recognized then the PDB-standard atoms IDs (N CA C O OXT CB) will be set for the main chain and beta carbon atoms and for the hydrogen atoms that they are bonded to. In addition, the ligand's atoms will be reordered so that the main chain atoms are first in the list. Currently, side chain atoms are assigned atom IDs using their numerical order (rather than PDB-style Greek letter remoteness codes CG CD CE etc). If you prefer for the renaming not to happen, then the new Grade2 command-line --no_aa_labels option turns it off, leaving standard numerical order based atom IDs. Note that, currently, no alterations are made if the input file specifies atom IDs (for example CIF restraint dictionaries and most MOL2 files). Please let us know if you would like this feature extended, for instance to set PDB-style Greek letter remoteness IDs for side chain atoms beyond CB. Thanks to Thierry Fischmann and Chip Lesburg for suggesting this extension. * A new Grade2 option --ocif is introduced to set the full filename for the CIF restraint dictionary. This allows the specification of the exact filename to be used for output. It is most useful when used with the --just_cif option. Thanks to Steven Sheriff for suggesting this option. * Grade2 should now deal with MOL2 files of charged molecules that have partial charges for atoms. To correctly identify the chemistry of a molecule the formal charge of each atom is required. This information is not stored in MOL2-format if partial charges are defined (the CSD-convention for MOL2 files is to use the partial charge field to store the formal charge). Grade2 now uses valency considerations to reconstruct the atomic formal charges if necessary. The fix has been tested with OpenBabel MOL2 files and copes with carboxylic acids, amines, imidazoles, nitro groups, azido groups, tetrazolates, isocyano groups, sulfanium groups, phosphonium and borates. Please let us know if you find a chemical group that causes problems. Thanks to Steven Sheriff for bringing the problem to our attention. * Grade2 should now correctly handle MOL2 files that use bond type ar for carboxylate groups. The CSD normalisation method can make a mistake when standardising the bonding of the group. Grade2 will now correct which oxygen atom carries the formal negative charge. Thanks to Dirk Reinert for reporting this bug. * Addition of a new automated refinement tool (aB_autorefine) that should make it even easier for new users to get started with BUSTER refinement. This tool runs a series of standard BUSTER refinements - from initial rigid-body to normal refinement with TLS, occupancy and ADP refinement including hydrogens (if appropriate). * The internal decision making at each step is reported together with the resulting BUSTER command-line: this can serve as a starting point for any additional fine-tuning by the user. * A final graphical summary is presented in a *_summary.png file for a quick overview of refinement progress. * Uses an experimental version of a variant of LSSR for NCS restraints (mainly by adding distance-dependent weighting). The original LSSR version can be activated by setting the parameter autoBUSTER_AutoRefine_NcsVersion=1 (to then behave identically to a stand-alone BUSTER "refine" job). Please note that this (for the moment) assumes that symmetrical side-chains (like GLU, ASP, PHE, TYR) maintain their NCS-relation - as they should if starting e.g. from a molecular replacement solution. Any "nomenclature correction" during model building should be avoided in such cases. * Activates the rejection of log-likelihood outliers throughout refinement - to exclude the worst reflection outliers. This can be deactivated via aB_autorefine_UseLogLikeFilteredMtz="no". * For details please see output of "aB_autorefine -h". * Significant improvement for refinements at high resolution (~1.1 A and higher) by adjusting the default blurring factor. The previous behaviour can be achieved via e.g. "refine blkblr=50 ...". * Several improvements in producing a PDBx/mmCIF file (BUSTER_model.cif) from BUSTER. This includes (1) the macromolecule as well as (2) potential restraint dictionaries. * Correction of missing _pdbx_refine_tls_group.pdbx_refine_id and _atom_site_anisotrop.type_symbol items. * Corrected inclusion of _chem_comp, _chem_comp_plane and _chem_comp_tor_value categories within restraint dictionary data blocks. * Better handling of AceDrg (undefined "chem_comp_tree" category) and eLBOW ("_chem_comp_bond.value_dist_neutron" item) dictionaries. * Ensuring that data categories and/or items not defined by current PDBx/mmCIF dictionary are prefix (e.g. with "gphl_" string). * Improved handling of C-terminal amidation: this should now be automatically recognised via an NH2 residue following the C-terminal amino acid. Thanks to Markus Rudolph for reporting and discussion. * Improved presentation of ice-rings in reciprocal-space correlation (RecSCC) plots: to avoid overlapping labels for high-resolution datasets (1.5 A and higher), only every 2nd resolution-marker label will be printed at the top of the plot. * Added option to pdb2occ (Pdb2OccRequireConsecutiveConsistency, default = "yes") that describes the way consecutive altConf residues are to be treated. The default ("yes") is to expect identical occupancy patterns for those consecutive altConf residues: setting this parameter to "no" will treat each residue as independent of the neighbouring ones (in case there is a different occupancy pattern). * Added option to BUSTER ("refine") to prevent occupancy refinement to fail if one of the atoms within an occupancy group has disappeared, e.g. through water update procedures: -occsum_skip_missing_atoms. * Added possibility to run alternate types of refinement within a single BUSTER run by activating/deactivating specific types of parameters (XYZ, B, OCC) at diffferent big cycles. The easiest way is to use the AlternatingRefinement macro to start with XYZ refinement and then alternate between B and XYZ+OCC strategies. * Consolidated consistency of non-bonded contact terms in BUSTER to ensure that the same values are used for hydrogenated and non-hydrogenated models (since those contact terms are mainly based on non-H atom distances). * Multiple developments resulting in significant speed-ups of refinement for large structures: * For diff_fourier (used in automatic analysis of anomalous and F(early)-F(late) maps) the peak location algorithm has been optimised. * The detection of non-bonded interactions during refinement has been reorganised. * Our internal tool for handling map peaks and atoms can use a boxing algorithm to speedup comparison. This can be activated by setting the environment variable PKMAPS_use_box to "yes". * At the end of a BUSTER refinement, two additional files ("summary.png" and "summary_LL.png") should be created in the "Plots" subdirecty (if ImageMagick is available as described in the installation instructions). These plots provide a summary of refinement progress and a detailed analysis of log-likelihood outlier reflections: interfaces to BUSTER could make use of those files and present them to the user. * Within Pipedream, Rhofit solutions will now be sorted by the correlation coefficient (to the mFo-DFc difference map). To restore the previous behaviour (sorting on internal Rhofit score), use the -nocorrelsort option to the "pipedream" command. ### Changes: * Modified the method for automatic adjustment of (relative) X-ray weight in BUSTER: instead of using as a default the same target rms(bond) (for standard residues) a resolution-dependent formula is now employed. This is based on large-scale data harvesting over a wide resolution range and should result in a better balance between X-ray and geometry part. There are three different variants available for this - triggered by the -rpolicy flag to "refine": "loose", "medium" (default) and "tight". In general, higher resolution structures will by default refine to a larger rms(bond) value (i.e. a higher weight to the X-ray term) while lower resolution structures will maintain a tighter geometry. The previous method of automatic adjustment can be used via the rmsBOND_method="old" parameter. * As a followup to allow lower-case chain names BUSTER now performs the comparison of set names in a case-sensitive manner. * Add geometric ANGLE restraint definitions of H{1,2,3}=N=CA for all peptide-like linkage types. * Add KCX to the list of amino acids to check for surplus hydrogen atoms in aB_hydrogenate. * Speedup the creation of pictures in the Plots subfolder by producing them via parallel execution. To deactivate set BusterCreatePlotsInParallel to "no". * Modifications have been made in Pipedream to ensure compatibility with the latest CCP4 8.0 release. ### Fixes: * Fixed problem whereby Grade2 restraint dictionaries could not be read by Coot because of long InChI records. The problem occurs because of long InChI records in the restraint dictionary, and it also occurs with CCP4-distributed restraint dictionaries. Currently, the CCP4 MMDB library (against which Coot is linked) places a line length limit of 500 characters, despite the IUCR CIF specification allowing lines of up to 2048 characters. We have let CCP4 know and the limit will be raised in a future CCP4/Coot release (by mmdb2 revision 56). From this release, Grade2 will no longer output long InChI records so there should be no problem in using Grade2 restraint dictionaries with older versions of Coot. Thanks to Steven Sheriff for bringing the problem to our attention. * A number of other small improvements and fixes to Grade2 have been made, as listed in the Changelog: https://gphl.gitlab.io/grade2_docs/changelog.html * An infelicity in the way Pipedream ran Phaser has been corrected. Phaser had been allowed to check for and potentially change the handedness of the input spacegroup. Although the potential for this behaviour to occur in practice is remote, it has now been corrected, so that Phaser can only use the spacegroup as specified. * Fix problem in aB_hydrogenate when encountering modified amino-acids within a macromolecule: surplus hydrogens (H2, H3) added at the peptide-bond nitrogen N were not always removed. Thanks to Steven Sheriff for reporting. * Fixed bug in plotting of ADP (ISOR) function values at end of BUSTER refinement (i.e. failing to create function_ADP_ISOR.png in the Plots subdirectory). * Fixup corner cases in the computation of angle restraint contributions (when an angle was exactly 0 or 180 degrees). * Switch off the automatic formfactor correction for H and He. * Fix reporting of B-values in screen output when ADP's are present. * Fix reporting of duplicate angle restraints. =================================================================== Improvements and fixes (released Feb 03 2022): * Grade2 Improvements and fixes: * A bug in the Grade2 --big_planes option has been fixed. The --big_planes option merges smaller planes into as large a single plane as possible. In the last release, this was done ignoring the sigmas (standard deviation of the out-of-plane distance) for individual restraints when merging them. The problem is that Grade2 produces weak planar restraints for torsion angles that, according to the CSD, have a moderate preference for planarity and these were then incorporated into a big plane. Weak planes (those with a sigma above 0.020 Angstrom) are now no longer incorporated into big planes. For further details, please see the "Treatment of Planar Groups" chapter of the Grade2 documentation: https://gphl.gitlab.io/grade2_docs/planes.html Thanks to Dirk Reinert for reporting this bug. * The ligand analysis performed within buster-report against the CSD (via Mogul) will now use a MOL2 file whose chemistry is based on the bond orders and atom charges given in the ligand's CIF restraint dictionary used in the refinement (after CSD standardisation). A tool based on Grade2 routines is used to write the MOL2 file, replacing the OpenBabel conversion that has proved unreliable. The chemical markup used in the CSD Mogul analysis should now correspond exactly to that used in restraint dictionary analysis. Thanks to Michael Blaesse and Dirk Reinert for reporting the problem. * A workaround allows Grade2 to be used with most recent CSD releases on both Linux and MacOS. There are problems with C-library duplication in the CSD Python API that previously prevented Grade2 working. We have let the CCDC know about the problems. * Grade2 now produces CIF restraint dictionaries containing both electron-cloud and nucleus X-H bond distance restraints, avoiding requiring separate restraint dictionaries for the two use cases. The --ecloud option is retained to specify that the ideal coordinates for the ligand should use the electron cloud rather than nuclear distances. The BUSTER refine option "-M Ecloud" can be be used to select the e-cloud model, or the option "-M HydrogenHybridModel" to select the hybrid model. * Grade2 has been altered to produce a single-plane restraint for each separate ring that is judged to be flat. Previously, planar rings were held flat by a number of four-atom planes. The --4_atom_planes option can be used to restore the previous behaviour. In practice, the change simplifies the restraint list but there is little difference in results. For further details, please see the "Treatment of Planar Groups" chapter of the Grade2 documentation: https://gphl.gitlab.io/grade2_docs/planes.html * Sorted bug whereby Grade2 would fail if the environment variable PYTHONPATH was set. Thanks to Yong Wang for reporting the problem. * Fix to Grade2 bug whereby, if given an input MOL2 file containing atom names with lower case letters, Grade2 went on to produce a restraint dictionary with unaltered atom names that could not be used in BUSTER. Thanks to Dirk Reinert for reporting this bug. * Grade2 now outputs information about which Mogul data libraries were used, and this information is included both in the terminal output and in the output CIF restraint dictionary in item _gphl_chem_comp_info.mogul_data_libraries. The CCDC releases periodic updates to the CSD throughout each year, and these will now be recorded. In addition, the use of Mogul information from in-house databases should also be logged. * Grade2 can now read eLBOW and Grade CIF restraint dictionaries as input files. As Grade CIF restraint dictionaries lack atom formal charge (_chem_comp_atom.charge) records, charges are set to zero when the restraint dictionary is read, and care must be taken as this may cause the output molecule to be incorrectly specified. * Grade2 now uses LIG for the default residue name (aka PDB chemical component id or 3-letter code). This follows the recent wwPDB announcement that LIG is now reserved for new ligands. Please see: https://gphl.gitlab.io/grade2_docs/faqs.html#output-residue-name * Most of the restraint dictionaries distributed in the common-compounds directory have been regenerated with the new Grade2 version. * FAQs have been added to the Grade2 documentation. The FAQs include "How can I run Grade2 if I only have a PDB file for the ligand?" and "How can I produce restraints for a ligand with a different protonation state or tautomer?" with a video demonstration. It is best to check the online version: https://gphl.gitlab.io/grade2_docs/faqs.html as this is frequently updated as new issues and questions come in. * Many small improvements and fixes to Grade2 have been made, as listed in the Changelog: https://gphl.gitlab.io/grade2_docs/changelog.html * Pipedream will now automatically determine the number of molecules in the asymmetric unit and will tell the Rhofit step to look for the appropriate number of copies of the ligand without having to be told. This behaviour can be overridden by explicitly setting the number of copies to look for with the -xclusters or -allclusters flags. * Added another fix-up function to aB_hydrogenate: the default Reduce binary (as e.g. distributed by CCP4) has hardwired hydrogen atom names for HEM that are no longer correct. These will now be adjusted automatically. * Added support for restraint dictionaries with both e-cloud and nucleus X-H bond distance restraints. This should work for those containing (in _chem_comp_bond category) items value_dist_nucleus and value_dist_nucleus_esd (e.g. AceDRG) or when only value_dist_neutron is present (and the value_dist_esd is used for both distances). The correct distance/esd value should be extracted according to the hydrogen model chosen (e.g. the e-cloud model with "-M Ecloud" or the hybrid model with "-M HydrogenHybridModel"). * Some additional compounds are now declared as being "boring" within buster-report (i.e. not analysed by default): PEG PGE TRS 1PE BME PPV CO2. To get reports for any of those compounds, please use the -interesting argument (see "buster-report -h"). * Fixes to computing real-space map correlation (e.g. within buster-report) for hydrogenated molecules: hydrogens are now treated separately to ensure main- and side-chain contributions are correctly pooled. * Make aB_plot_logLikelihood aware if a non-standard test-set flag value is used. * Fixes in writing final MTZ file (refine.mtz) - to ensure that the correct wavelength and dataset name is written into the header. Improvements and fixes (released Oct 10 2021): * Added support for double-quotes (") in atom names within the restraint dictionary handling of Grade, Rhofit and BUSTER. * Added support for user-defined restraint dictionary location (via UseDictionaryCommonCompoundsOwn parameter pointing to a directory with XYZ.cif files) to geometry-only refinement (gelly_refine) tool. * Fixes to the handling of user-provided restraint dictionaries to support compound names like "%01". The compound names "%01" to "%99" are defined by the wwPDB as a reserved series that will not be used by the wwPDB archive itself, so depositing a structure with compounds or ligands using that residue name will clearly be marked as a potentially new compound and not clash with an already taken identifier (like "LIG" that is used in 1JVP). These changes affect the restraint generation with Grade, ligand fitting with Rhofit and refinement with BUSTER. Thanks to Steven Sheriff for reporting and discussions. * Fixes to MakeLINK in generating connectivity information (so-called TNT sequence file): * added support for CRO residue * improved automatic determination of residue class (amino-acid, DNA, RNA etc) These should lead to a significantly lower number of failed refinements, especially with a "duplicated bond restraints" error. Initial tests suggest this could have fixed about 50% of previously stopped BUSTER refinements. * Fixed problems with aB_fuseplanes tool and Grade2 dictionaries. * Fixed problem with water molecule counting within the "analyse" tool (creating the analyse.html file if requested). Thanks to Steven Sheriff for reporting. * Fixes to buster-report to better support MapOnly-refinements. * Correction of a bug in aB_deposition_combine that caused failures on MacOS systems (thanks to Mike Norris for reporting). * The Pipedream standard output has seen a few minor formatting changes and consolidation regarding the number of empty lines printed. Improvements and fixes (released Jul 16 2021): * Grade2: The initial release of the new restraint generation tool, written by Oliver Smart. Grade2 is a clean-slate reimplementation using ideas from Grade, using the CSD Python API and the RDKit toolkit. Grade2 already has several advantages compared to Grade: 1. Grade2 makes better use of CSD information for rings and planes, using the CSD Python API to extend Mogul analysis. 2. Grade2 can handle a wider range of elements. 3. Grade2 is more robust. In a recent test of generating restraints-dictionaries for 2893 chemical components recently added to wwPDB, Grade2 produced dictionaries for all but 6 (0.2% failure) whereas Grade failed in 336 cases (12%). 4. Grade2 protonates or deprotonates groups commonly charged at neutral pH such as carboxylic acids, phosphates and alkylamines. 5. Grade2 provides a good starting point for future developments. Internal testing has shown improvements in the description of molecular geometry (via restraint dictionaries) through improved estimation of ESD's. We therefore expect refinements using Grade2 dictionaries to behave better and be more consistent across different types of chemistry. Grade2 is included in this BUSTER release alongside Grade. Please use "grade2 -h" or see the full documentation: $BDG_home/docs/grade2/html/index.html for details. As is the case with Grade, Grade2 is only supported on those operating systems that are also supported by the CSDS. Any feedback about the performance of this new tool would be highly appreciated. * A new feature to use a so-called "hybrid model" for hydrogen treatment has been added. This can be activated via the "-M HydrogenHybridModel" macro and will use hydrogens at the nuclear position for the geometry and at the electron-cloud position for the X-ray term, respectively. The input model could be prepared via aB_hydrogenate using the "-full" command-line argument. The output file from a BUSTER refinement will contain hydrogens with full occupancy at the nuclear position. * Fixes to hydrogenation tool aB_hydrogenate - in functions to correct errors from the initial step (Reduce as called by "hydrogenate") related to incorrect occupancy values as well as alternate-conformation confusion. Thanks to Dirk Reinert for reporting and providing a test case. * Plots of the log-likelihood and Z-score on a per-reflection basis at the end of a refinement are now included in the X-ray section of buster-report. They are generated using the new aB_plot_logLikelihood tool and can initially be used for diagnostics. Follow-up work will provide a facility for automatically excluding from refinement outliers beyond a given log-likelihood threshold. * In order to further stabilise the scaling during refinement restrict the allowed range of some of the scaling parameters. * Fixed an issue on macOS for aB_plot_RecSCC such that plots again have meaningful colors. Thanks to Oliver Smart for reporting and discussion. * Even when refining against one of the so-called "early" or "late" datasets (as generated by autoPROC), allow generation and analysis of the radiation-damage detection (F(early)-F(late)) maps. * Pipedream will now not refine the TLS parameters in the -L run and will ensure that the resolution limits match those at the end of the previous full refinement (version 2 protocol only) * Pipedream will now accept an autoPROC summary.tar.gz file as a valid input for the -autoprocdir option. * Pipedream will now deal with multi-sweep datasets with small differences in wavelength more robustly. * Further development of the Pipedream JSON output file. Thanks to Raphael Bourgeas and Yorgo El Moubayed. * Several fixes to aB_cif2table1 (see also https://staraniso.globalphasing.org/table1/) to restrict to models based on diffraction data. * Improved visualise-geometry-coot so that it should now also run from inside a buster-report output directory (in the same way that it does from inside a BUSTER/refine output directory). * Some changes to buster-report regarding output information: an overall wall-clock execution time is now displayed at the end of a successful run and the detailed CPU time information for various individual steps is only given with increased verbosity (-v flag). * Within buster-report we now use the aB_hydrogenate wrapper tool instead of directly calling hydrogenate: this way all the fix-up functionality provided by aB_hydrogenate will also be available for the PDB file used in the ligand analysis via CCDC/Mogul. * To have individual MolProbity commands (like molprobity.clashscore etc) behave more similarly to the molprobity.molprobity command (part of CCTBX as distributed with CCP4) within buster-report, the input PDB file will first go through the new aB_fix_h_occ tool to ensure that zero-occupancy hydrogens are changed to full occupancy (i.e. same as that of the parent atom they are connected to). This is to prevent those zero-occupancy hydrogens from being invisible to e.g. the molprobity.clashscore command while they are modified in the same (or very similar) way when passing through the master command molprobity.molprobity. * The AddMissingSsbondRecords=yes setting has been made the default, so that missing SSBOND records with unambiguous disulfide geometry (as determined via our ana_ssbond tool) will be automatically added. This can be prevented by setting AddMissingSsbondRecords=no - or by providing an input model with correct SSBOND information. NOTE THEREFORE that if the lack of correct SSBOND records on input is/was the main reason for setting StopOnGellySanityCheckError=no in your "refine" commands or scripts, we recommend removing that StopOnGellySanityCheckError flag again (or setting it to "yes"). Most checks performed at that stage will then only create a stopping error if there is some serious problem with the interpretation of connectivity within the input structure, therefore providing potentially important feedback to avoid producing distorted structures on output. * Fixed renaming of _chem_comp_chir.atom_id_N to _chem_comp_chir.gphl_atom_id_N in aB_deposition_prep. * Fix to "fetch_PDB" when encountering reflection data files missing the _refln.wavelength_id column. Improvements and fixes (released Apr 20 2021): * Added two new tools to move between C2 and I2 settings ("aB_I2_to_C2" and "aB_C2_to_I2") if needed. * Replaced previously provided Gnuplot binary with a version that should improve timing on CentOS 8 systems. * Small speed-up in the MTZ-checking step of a BUSTER ("refine") job by (1) switching from the CCP4 MTZDUMP to our own MTZANA program, and (2) by buffering the relevant info if applicable. * Improvement in handling multiple -RB flags (with different or no resolution values attached to each rigid-body step). * Improved handling of models with existing hydrogens when running aB_hydrogenate: if the -full flag is explicitly given (i.e. indicating that added hydrogens should have the full occupancy of the parent atom), any existing hydrogen will have its occupancy adjusted as well. This will avoid carrying hydrogens over with their initial occ=0.0 value, which seems to go against the user's intention in this case. * Fixes and improvements in handling of real-space map correlation in buster-report: compounds with alternate conformation identifier should be treated correctly now. Thanks to Paul Rowland for reporting. * Fixed regression (introduced in Oct 2019) which resulted in the automatic low-resolution restriction reported (due to poor reciprocal space correlations at the lowest resolution range) not being actually acted on. * Fixed regression in printing additional useful information about optionally rotated symmetrical side-chains (via -sim_swap_equiv flag) as well as LSSR pruning during NCS setup. * Pipedream will now write out a summary of all the significant data in json format (pipedream_summary.json), in addition to its xml formatted output (summary.xml). * Added new tool ("aP_xml_to_json") to convert autoPROC xml output files to json format. Improvements and fixes (released Feb 24 2021): * Pipedream: A significant update (version 2) of the pre-Rhofit refinement protocols has been implemented. The main reason for the change is to separate the addition of solvent from the process of ligand density elicitation (the -L protocol in BUSTER), while at the same time providing a framework for future developments regarding different refinement strategies. The refinement steps prior to ligand fitting concentrate on convergence and a thorough update of the solvent model (including addition of 2nd shell waters) with a separate BUSTER run to look for and describe potential ligand binding sites. The ligand complex model after Rhofit will bring only those "genuine" waters into the final refinement step. For full details of the available refinement protocols please see chapter 2 and appendix B in the Pipedream documentation. Extensive internal testing of the new protocol has shown improvements in overall performance and outcomes, ranging from lower R/Rfree, better ligand placement and improved geometry, in the majority of cases. It should also be noted that despite the inclusion of an additional BUSTER run, the impact on the overall time taken by Pipedream is relatively small, largely due to better enforced convergence providing for better decision making and a faster path to the final complex structure. The previous (version 1 up to the 20201211 release) pre-Rhofit refinement protocols can still be run by using the new -v1 command-line option. * As part of our activities within the wwPDB's PDBx/mmCIF Deposition SubGroup on Data Collection/Processing, we have defined new dictionary items (over 50 in total), complete with detailed descriptions, that have now been incorporated into the official PDB Exchange (PDBx/mmCIF) Dictionary that supports deposition to the PDB - see : https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/ Their purpose is to facilitate the deposition and archiving of certain types of diffraction data, as well as accommodate new quality metrics pertaining to these data. These extensions cover three areas: 1. merged reflection data that have been processed to take account of diffraction anisotropy, with descriptors for that anisotropy, for the cut-off criterion applied to the data, and for the ellipsoid fitted to the cut-off surface; 2. unmerged reflection data, providing extra item definitions aimed at improving support for the deposition of such data and at ensuring that they can be meaningfully reprocessed after retrieval from the archive; 3. anomalous diffraction data and associated statistics. All along this work, we have made sure that deposition-ready mmCIF files produced by our software (autoPROC and BUSTER) take advantage of these new definitions and validate against the updated mmCIF dictionary. As a consequence, users are very much encouraged to upload these files directly to the PDB for deposition, and thus avoid the MTZ + PDBEXTRACT route. We thank the PDBx/mmCIF Deposition SubGroup on Data Collection/Processing, and especially Ezra Peisach and John Westbrook, for their energetic and constructive engagement with this effort. * If Pipedream was started from raw images, the final deposition-ready coordinate and reflection mmCIF files will also contain the additional reflection data and processing information (including all data quality metrics) from the autoPROC processing step. * Pipedream will now report the number, approximate volume and location of "interesting" sites (potential ligand sites) located by the -L option of BUSTER as well as the number of waters present after both pre-Rhofit refinement and post-refinement steps. * A new option to "pdb2occ" allows specification of residues that should be ignored during the generation of occupancy-refinement specifications. This complements the -r flag and supports the use of residue names (e.g. "HOH") as well as residue identifiers (e.g. "A|4000"). * A new option to the "hydrogenate" and "aB_hydrogenate" commands allows finer control over the handling of hydrogens already present in the input model. The default is to leave those as-is, but with "-adjust" their X-H distance can be adjusted to the (idealised) value according to the model used (ecloud or nuclear). Note: the current version of REDUCE has a problem in that so-called "rotatable" hydrogens (e.g. attached to SER-OG, CYS-SG, LYS-NZ, TYR-OH) are still adjusted even if told not to do this. A proposed patch has been submitted to the official REDUCE repository (https://github.com/rlabduke/reduce). * Improvement to aB_hydrogenate in order to handle non-standard amino-acid hydrogenation (at N-terminal amino group) better: more known unusual amino-acid residues are now recognized and handling of residues within a chain (as opposed to only at N-terminus) has been added. * Added extraction of experiment and software information from PDBx/mmCIF files within the aB_cif2table1 tool (to give a fuller picture and context to the data quality metrics). * Please be aware that CSD 2021 is currently unsupported on MacOS 11 (Big Sur) and therefore Grade (grade and grade_PDB_Ligand) as well as buster-report are not supported on that platform. Support for MacOS 11 is expected in a forthcoming update to CSD. * Fixes in Rhofit to treat overlapping waters in final merged PDB file correctly (the information about close waters given in header of the fitted ligand PDB files was not always complete). * Fixes in Gelly to handle alternate conformation information for atoms correctly in both refinement mode (when using targeting) and ligand-fitting (Rhofit). * Fix in aB_cif2table to provide better error messages (Thanks to C.-S. Huang for reporting). * Fixed regression when using non-BUSTER maps for Rhofit ligand fitting: MTZ column names other than FOFCWT/PHFOFCWT and 2FOFCWT/PH2FOFCWT were not recognized (reported by K. Battaile). Improvements and fixes (released Dec 11 2020): * The reporting of R-factors has changed: the default now is to use R-factors (work, free and all) based on Fcalc, similar to other refinement programs. The previous behaviour (using the expectation value <|Fcalc|>) is accessible through the flag autoBUSTER_RvalueType=FX. Please note that always both types of R-factors are computed and that one can do so separately by using e.g. our "rvalue" tool. * Added new check (PdbChk_RemoveMetalFromLink) to "pdbchk" that will remove LINK records containing metals. These could be describing metal coordination (which might be useful to restrain), but should not be mistaken as a covalent bond at this stage. * Improved handling of automatic X-ray weight adjustment: check that there is at least a significant change in BOND function value (AdjustXrayWeightSignificantChangeBondFunction=2, in percent) to justify a change in weight. * Added full support for restraint dictionaries that have a separate _chem_comp_bond.aromatic flag and Kekule types ("single", "double") for the individual bonds * Added a series of new tools to handle generation of various plots of a particular BUSTER run: aB_plot_RecSCC : reciprocal-space correlation aB_plot_funtag : various function values aB_plot_mapcc : real-space map correlation per chain/residue aB_plot_opttag : progress of optimisation aB_plot_rvalue : R-values (R-work and R-free) aB_plot_scatag : scale parameters aB_plot_wilson : relative Wilson scaling These tools are called automatically at the end of a BUSTER run (this can be switched off via BusterCreatePlots=no), creating PNG files in a subdirectory "Plots". The program Gnuplot will be used for generation of these graphs, removing the need for installing Xmgr/Grace and therefore simplifying installation. The "buster-report" tool has been changed to take advantage of these plots directly when generating its HTML or PDF reports. Please note that especially the real-space CC plots have been modified to take NCS-relations into account. Note also the complete redesign of the presentation of CC values, that now uses curves instead of barcharts. * Additional helper packages for OpenBabel and PyMol are now included. For OpenBabel we provide both Linux and Darwin binaries. For PyMol we initally provide binaries for CentOS-7 and CentOS-8. Two new wrapper tools, aB_obabel and aB_pymol, are provided to make use of the new helper packages. * A new tool (aB_cif2table1) to analyse a given PDBx/mmCIF file and extract the data processing statistics (merging statistics, i.e. data quality metrics) into a easily readable file (ASCII text or HTML). * The new tool aB_ana_cluster can be used to to give more information about a particular (so-called) cluster. This is used e.g. in Pipedream to provide the user with information about size and location of potential ligand binding sites. * To provide more flexibility for the generation of larger planar restraints in compound dictionaries, aB_fuseplanes can be run on a standard Grade dictionary (other restraint dictionary generator output might also work, bus this has not been extensively tested). The different overlapping, small (usually 4-atoms) planes are then combined according to user-provided recipes and flags, e.g. growing planes only within ring systems. Thanks to M. Blaesse for providing suggestions and feedback. Please check the resulting restraint dictionary e.g. with our "EditREFMAC" tool (this requires Java). * New option (-fixupcif) for both 'grade' and 'grade_PDB_ligand': this will ensure that sp2 (aromatic) ring carbons have an active planarity restraint independent of the ability to deduce this information from either CSD or QM. Thanks to V. Rangel and M. Zebisch for highlighting and discussing this. * The CSD analysis within buster-report (via Mogul) has been stabilised by switching to a MOL2 version of the ligand investigated: the original PDB format showed some incorrect handling of hydrogenation within Mogul in some cases (thanks to M. Blaesse for providing feedback and examples). The previous behaviour can be forced by setting the environment variable $BDG_MOGUL_USE_PDB to a non-empty value. * Improved the hydrogenation tool "hydrogenate" (also called from the aB_hydrogenate wrapper script) to work for simpler input PDB files (e.g. ligands or compounds) that contain only ATOM or HETATM cards. * Fixed handling of atom names containing single quotes ("'") as part of the atom name - and are therefore double-quoted in mmCIF restraints dictionary files - in EditREFMAC plane restraints tab. Improvements and fixes (released Sep 18 2020): * New tool to help creating a single, deposition-ready mmCIF file from data-processing and refinement: aB_deposition_combine. This has been developed and tested against autoPROC-processed data - in which case it will (1) extract the data scaling and merging statistics from the processing step and place them into the model PDBx/mmCIF file from BUSTER (2) combine the reflection data from BUSTER with the upstream reflection data from processing (which can contain additional data like anomalous differences, F(early) and F(late) amplitudes, scaled and merged intensities before application of a cut-off etc). * Added fixing function to aB_hydrogenate to ensure that an existing C-terminal oxygen (OXT) atom as given on input is *always* at the end of the final residue in the resulting PDB file after hydrogen addition. * Detect IOD as an ion. This avoids occasional failure due to the atom not partaking in any bonds. * Fix in PKMAPS (tool to perform comparisons between coordinates from coordinate or map files) to avoid incorrect assignment of "identity" of coordinates. This could have an impact in water update as well as the aB_pdb_1and2/aB_pdb_1not2 tools. * Clarify whether refinement has converged or not in the "clipping" messages. * Fixed regression regarding hydrogen occupancy handling (introduced in previous release when improving behaviour of initial scaling). * Fixed regression that made "visualise-rhofit-coot" not work in the previous release. * Corrected an issue in buster-report to avoid failure if the absolute path for the output directory is specified (thanks to Dirk Reinert for reporting this). * To check functionality of buster-report within "checkdeps", no output file for the MolProbity check needs to be generated. * Fixes to visualise-geometry-coot when running on buster-report output: the probe dots generated by MolProbity are now correctly displayed. * Simplified and enhanced external Pipedream dependencies by removing the need for the List-MoreUtils Perl module and including a new Perl XML module (TreePP) in the distribution to allow reading and interpretation of XML data files as generated by the various internal pipeline components. * Pipedream now reads and displays the appropriate "Table 1" (merging statistics and data quality information) directly from autoPROC in the summary.out file. It also reads and includes the autoPROC ISPyB compatible XML output in summary.xml. This ensures that a more extensive report of autoPROC output is produced in the same format as by autoPROC itself. * A conservative change has been made to the pre-Rhofit refinement protocols to correct a minor issue in the use of the -L and -WAT options. The modification does not result in any change of behaviour. * Ensure that summary.xml is always correctly closed regardless of the termination state of Pipedream. Improvements and fixes (released May 20 2020): * Updated buster-report to use the latest cctbx-based version of MolProbity, from the CCP4 distribution. The output from this version of buster-report is similar to that of the previous release, for maximum compatibility. However, the colour coding of the MolProbity statistics is no longer generated and the per-residue list of MolProbity parameters is also no longer generated in the html output. In its place, a Coot script is automatically generated to allow interactive navigation to outliers in Coot. Use of the old version of MolProbity (4.0.2) has now been deprecated and will be removed completely in a future release. In the meantime, buster-report can be instructed to use MolProbity 4.0.2 by use of the command-line option -oldmp. * visualise-geometry-coot has been updated so that it will automatically load the MolProbity script if run with a buster-report output directory. * Pipedream has been updated to report additional autoPROC and BUSTER statistics in both the summary.out and summary.xml files. In addition it will also report the MolProbity and ligand analysis statistics. (Thanks to Dirk Reinert for the request). Please note that inclusion of the additional information has necessitated some format changes to the summary.out file. If you parse summary.out to extract information, you may need to update your parser due to these changes. This is why we would recommend the use of the summary.xml file instead. * Improve the generation of TLS information in mmCIF files. We now also write pdbx_tls_group_id in the atom_site block. The information in the pdbx_refine_tls_group block is now being filled in when applicable. * It is now possible to use insertion codes in a residue range specification. * Added another fixing function to aB_hydrogenate (our recommended hydrogenation tool) - which runs on top of "hydrogenate" and ultimately Reduce (from the MolProbity tool): newly added hydrogens might exhibit alternate conformation patterns inconsistent with the parent heavy atom. This seems to be related with alternate conformations of a preceeding residue which is confusing Reduce as far as we can see. * Added feature to "aB_covalent_ligand" (tool to generate restraint dictionaries for covalent modifications) to allow users the use of the Grade server (grade.globalphasing.org) if no local CCDC/CSD installation is available. This requires a few additional manual steps (described in detail when running this tool interactively with the new "-server" flag). Thanks to K. Bataille for suggestions and discussion. * Added support for downloading CIF-only PDB entries with the "fetch_PDB" tool. These are then converted into PDB (if at all possible) using Gemmi. * Added information about hydrogen model used during refinement into output PDB file (REMARK 3 section). The different modes of hydrogen handling at the point of refinement will be recorded (if hydrogens are present in input): are they refined against electron-cloud (closer to parent atom) or nuclear distances (actual position of the hydrogen atom) and are they used with zero or full (i.e. same as parent atom) occupancy. * Fixed handling of ANISOU records in the "Boolean operation" tools aB_pdb_1and2, aB_pdb_1close2 and aB_pdb_1not2: those records where previously lost. * Fixed regression in the treatment of occupancies of hydrogen atoms. Occupancies of hydrogen atoms that were meant to be set to zero were set to zero after the first scaling round. The impact could sometimes be seen as an apparent jump in R-values. Improvements and fixes (released Mar 19 2020): * New feature in BUSTER to stabilize the refinement when TLS is involved. This is controlled by a new parameter (TLSfreeze) that switches off concurrent refinement of certain classes of variables in the big cycles that refine TLS parameters. The default (tls:B) will keep individual atomic isotropic B-factors constant. See appendix1.html for additional details. This feature reduces the number of "clipping" messages, which in some instances could make the refinement stall. (Thanks to D. Reinert for providing a test case and additional information). * Fix memory access bug that caused refine to issue PETSC ERRORs and occasional crash during the final geometry/screen analysis to generate screen_final.txt. * For PDB output swap a possible charge in cols. 79-80 to write magnitude followed by sign. This to make it easier to interact with eg. RDKit. * Updated Grade and grade_PDB_ligand - a small change to how Mogul is run to increase the number of restraints set from Mogul and reduce the number set from QM. Improvements and fixes (released Feb 06 2020): * Pipedream now creates a status file in its output directory, which is updated as the job progresses. The status of a running Pipedream job can be determined by looking at the last line of the status file. * Minor updates to Pipedream for compatibility with the upcoming release of CCP4 version 7.1. * Modified default handling of non-Grade CIF dictonaries within BUSTER: previously, torsion angles of such restraint dictionaries were ignored by default (but kept for monitoring). This was due to poorer (non-Grade) dictionary quality for this type of restraints at the time. This behaviour has now been changed and all torsion angle restraints will be used as-is independently of the dictionary provenance. To re-instate the previous behaviour, set BelieveAllTorsionRestraints to "no". * New water handling macro ("-M WaterUpdate2ndShell") to allow for 2nd-shell water addition as well as slightly shorter contact distances for newly placed waters (down to 2.15A). The settings for the WaterUpdatePkmaps macro will now be also triggered via the simple "-WAT" command-line flag. To revert to the previous behaviour, please use refine ... \ -WAT WaterPickingHydrogenPartner="no" WaterMinDistance=2.5 \ ... * Updated heme dictionaries for HEM (heme b) and HEC (heme C) - including the covalent linkage definition for Cys-SG to HEC. * Adjusted NONMETALBump parameter in hydrogenate script to prevent issue with reduce not adding a hydrogen in case of a close contact. * Allow specification of PDB file and compound dictionary via the more common -p/-l flags also for aB_hydrogenate (Thanks to S. Sheriff for pointing this out). * Make supporting up to 3 alternate conformations in pdb2occ the new default (previously, only up to 2 alternate conformations would have triggered generation of a "NOTE BUSTER_OCCSUM" restraint - to keep the sum of all occupancies at 1). The parameter Pdb2OccMaxAlt can be changed (e.g. to 2, 4 etc) to modify this behaviour. (Thanks to S. Sheriff for highlighting this). * Improve gelly to detect specification of empty TLS sets. * Improve the detection of erratic set specifications when converting TLS selection records using pdb2tls. * Fixed regression in the reporting of R-values when a non-standard test-set flag value is used (Thanks to J. Sack for reporting this issue). * Improved handling of occupancy refinement to ensure that (1) final coordinate files don't contain summed occupancies above one and (2) hydrogens will have the same occupancy as their binding partner on output. Thanks to S. Sheriff and D. Reinert. * When encountering alternate conformation residues that have different occupancies (within an alternate conformation), pdb2occ will now skip defining an occupancy refinement instruction for those. A (hopefully) meaningful warning message is provided to the user in order to correct the underlying issue within the coordinate PDB file itself. * Added simple switch to use the CCP4 distributed compound library as a (final) fall-back when setting up all compound restraints: the parameter UseCcp4MonomerLibrary (default = "no") can be set to "yes" to provide a restraints dictionary for a compound that is not part of the BUSTER distribution, not provided directly by the user (via the "-l" command-line argument) or not present in a user-specified monomer library (pointed to via the UseDictionaryCommonCompoundsOwn parameter). * Updated the BUSTER manual in multiple places ($BDG_home/docs/autobuster/manual/autoBUSTER0.html). * Bug fixes in Pipedream checkdeps. * Fixed wrong warning message analysis in pdb2occ. Improvements and fixes (released Dec 17 2019): * Added support for lower-case chain identifiers in PDB files in BUSTER ("refine") - thanks to S. Harris and H. Schreuder for highlighting this. * As announced for the Sep 20 2017 release, the -nomogul option to "grade" and "grade_PDB_ligand" has been removed. This option allowed for the generatation of compound restraint dictionaries without access to the Cambridge Structure Database (CSD) via the mogul program. You now must have a functional installation of the CSD in order to run grade and grade_PDB_ligand. For users without access to a local CSD installation, the Grade server at http://grade.globalphasing.org/ can be used for generation of restraint dictionaries (also compatible with other programs). * Added functionality to aB_hydrogenate to fix atom naming convention for ADE residue (where the current CCP4-distributed version of reduce uses non-standard hydrogen atom names). Improvements and fixes (released Nov 29 2019): ################################################################## ## Pipedream - CHANGE TO DEFAULT!! ## ## When run from images or from the output of a previous autoPROC ## job, Pipedream will now default to using the anisotropically ## analysed and scaled output file from STARANISO for all further ## steps (i.e. staraniso_alldata-unique.mtz). The -useaniso option ## has been retained for backwards compatibility but is no longer ## required. The -useiso option has been added to force use of the ## isotropically analysed output data from autoPROC ## (i.e. truncate-unique.mtz). ################################################################## * Improvement to aB_hydrogenate to ensure disulfide bridges are not accidentially hydrogenated when they involve symmetry or are at large distance (SG-SG above 2.3A). That means that any disulfide bridge defined with a complete and valid SSBOND card will be excluded from hydrogenation (HG atom on SG) independently from the decisions taken within "reduce". At the same time, alternate conformation CYS residues will be allowed to carry HG hydrogens (if this alternate conformation has an SG-SG distance above 2.3A): we then assume that these represent a partially broken disulfide bond. Thanks to A. Hruza for reporting. * Further improvements to the handling of resolution limits (especially low-resolution limits) correctly - covering data limits in input MTZ file, user-supplied limits (via 'refine -R' flag) and available numerical precision. This should avoid dropping a single or very few low-resolution reflections along the way from input to final output MTZ file (and reporting). * Multiple improvements to Grade (dictionary generator): * Introduced a fingerprinting system for 4-atom planes. There are two types of 4-atom planes defined within Grade: (1) so-called trigonal 1-4 planes with a central atom and 3 bonded atoms (e.g. sp2-carbon); (2) so-called torsional 1-4 planes with 4 atoms connected in a 1-2-3-4 manner; The fingerprints are currently used in greylisting, i.e. excluding certain types of chemistry from being considered for these 4-atom planar restraints: (a) torsional 1-4 planes coming from CSD (via Mogul) (b) torsional 1-4 planes coming from QM (c) trigonal 1-4 planes coming from QM It is mainly (b) where this will have an effect at the moment. The fingerprints consist of element, hybridisation and bond-type information - and look similar for trigonal and torsional 1-4 planes: trigonal :

==> atom 1 is the central atom, other atoms are sorted (in increasing order) based on "" torsional :

==> the atoms are given in "bonding order" (1-2-3-4 or 4-3-2-1) where = element symbol for atom i (e.g. C, N, O, S etc) = hybridisation of atom i (e.g. 2 for sp2, 3 for sp3 and 0 for unknown) = bond type between atom i and atom j (s=single, d=double, t=triple, a=aromatic) For example, the torsional 1-4 "plane" in DMF for atoms O=C-N-C1 would have the fingerprint O2dC2sN2sC3. See http://www.rcsb.org/ligand/DMF for exact atom naming. Another example would be the trigonal 1-4 "plane" in 8PM for atoms C15 \ N14-C21 / S1 which would get the fingerprint N2sC3sC3sS0. See http://www.rcsb.org/ligand/8PM for exact atom naming. We have seen issues concerning the 4-atom planar restraint generation by Grade mainly for MOL2 files from CORINA (either via the deposited "ideal coordinates" at Ligand-Expo or MSDchem, or from in-house systems also using CORINA). Other routes (especially via SMILES strings) seem to behave better in that respect. Thanks to M. Blaesse for triggering this investigation! * Ensure that various intermediate steps/tools within Grade transfer the bond type information correctly to all subsequent steps. * Fixes to grade-ciftool component to use the minimum number of required CSD samples consistently across bonds, angles and torsions. Also fixed the analysis of the torsion angle distributions in distinct bins as given by Mogul. * Fixes to the "EditREFMAC" tool for visualising restraint dictionaries to also work with Acedrg-generated files (e.g. those in $CCP4/lib/data/monomers/[0-9a-z]). Please let us know if any particular dictionary files still give problems. * BUSTER and its associated programs will now run under the latest release of macOS - 10.15 (Catalina) - with one exception: * The version of Molprobity currently required by buster-report is not compatible with macOS 10.15 as it contains 32-bit binaries. We are looking to replace this version of Molprobity with the newer cctbx based version that is now distributed with CCP4 and we will update buster-report as soon as possible. * In the meantime, buster-report can still be run, but without Molprobity. In order to tell buster-report that Molprobity is not available, the environment variable BDG_TOOL_MOLPROBITY_ROOT should be set to "none" - see the macOS installation instructions for details. * Fix regression introduced in September 2019 that made harvest report some low resolution limits with reduced precision. Thanks to J. Kopek for reporting this issue. * Fix argument handling in gelly_refine (that could cause problems for grade or grade_PDB_ligand when BUSTER installation directory has a very long PATH). * Fixed cases where aB_hydrogenate would not report where restraints where obtained from. Thanks to D. Reinert for reporting this issue. * Added column name "RFREE" to automatically recognized list of allowed test-set flags in the input MTZ file. * Improvement to the handling of non-standard test-set flag column names in the input MTZ file. Thanks to W. Tempel for reporting. * Fixed regression in rvalue tool (for computing R-values) if called stand-alone with a BUSTER MTZ file that includes DFc-completion value for the 2mFo-DFc map coefficients. * Fixed regression introduced in October 2018 that resulted in the last reciprocal space correlation plot as shown in buster-report output actually being the one from the beginning of a big cycle (and not from the end when refinement has converged). * Improvement to LSSR-targeting in refine by allowing a path length longer than 100 characters. Thanks to J. Ruprecht for reporting. * Improve buster-report to also copy BUSTER_model.cif and BUSTER_refln.cif files to results directory. * Improvement to grade-ciftool by removing spurious carriage-return (CR) characters from comments. Thanks to J. Kopek for reporting. * Improvement to grade and grade_PDB_ligand so they report appropriate version(s) and date(s). * Fix to grade_PDB_ligand so that ligand names enclosed in double quotes no longer lose the last character of the name. * Really fix grade_PDB_ligand to deal with URL changes at EBI. Thanks to K. Battaile for reporting. * Fixes to fetch_PDB to handle _diffrn_refln loops in mmCIF files and to catch a missing CCP4 setup. Improvements and fixes (released Oct 3 2019): * Added explicit hydrogen-hydrogen contacts for hydrogens at electron-cloud or nuclear position. The atom-type specific contact distances are based on Williams et al (2018, https://dx.doi.org/10.1002/pro.3330). This should avoid explicit hydrogens moving too close to each other (because too short a contact distance was assumed as a default). When running hydrogen-based clash analysis e.g. via MolProbity it is recommended to use the explicit hydrogens as refined and output by BUSTER, e.g. via molprobity.clashscore keep_hydrogens=True (also use the correct nuclear=False|True parameter depending on your hydrogen model: nuclear position or electron-cloud position). Thanks for D. Reinert for discussions. * Added missing torsion angle restraints to the Engh&Huber amino-acid restraint dictionary involving hydrogen atoms (to ensure staggered conformation of e.g. methyl groups). * Improved aB_hydrogenate script to give detailed information about dictionary provenance for actual hydrogenation step. * Better weights for (new) B-factor restraints database: a lower weight (halved from the previous value of 20) should avoid over-restrained B-factors for BUSTER-refined structures. Please note that this is an active area of development and is likely to further improve in the near future. * Fixed regression in previous release whereby the automatic resetting of the low-resolution limit due to bad correlation had been inactivated. * Fixed regression introduced in 2017 that made buster-report not work correctly on MapOnly result directory. * Fix to the 20190607.macro to use the correct filename for the old B-correlation restraints file (bcorrel_20190607.dat). Thanks to K. Longenecker for noticing. * Fix to avoid shaving off a single low-resolution reflection when defining the resolution limits (from input MTZ file and/or user-supplied) for BUSTER. * Fix to the detection and handling of pseudo-chiral centres (which resulted in a regression in the previous 20190923 release) with regards to dictionary restraint generation with Grade. Thanks to D. Reinert for analysing and discussing this. * Fix an issue where the final MTZ file contains dummy indices to higher resolution than the data used for refinement. This could happen when BusterAnoFourier="yes" and/or BusterEarlyLate="yes". Thanks to Robert Byrne for reporting this issue. * Fix to grade_PDB_ligand to deal with URL changes at EBI. Thanks to V. Calderone for reporting this. * Fix to buster-report to also detect obabel version 3 and above. Thanks to V. Calderone for reporting this. Improvements and fixes (released Sep 23 2019): * Stage one of a major overhaul of the handling of contacts within the structural model. The previous system of element-specific (reduced) van-der-Walls radii was too simplistic in accurately describing the actual chemistry especially for 1-4 contacts (i.e. contacts along a torsion angle). The parameters employed for those 1-4 contacts resulted in too restrictive distances along those contacts with a knock-on effect on rotamer conformations, i.e. pushing side-chains from an allowed/favoured rotamer conformation into an outlier conformation if the electron density is not strong enough. This first versions includes several new or changed features: (1) Moving towards atom-type specific distance restraints (instead of the more generic element-type version) to allow for finer detail. (2) Actual target distances (and sigmas) are based on a large scale analysis of 30718 PDB structures (as of 20190115) with resolution better than 2A, low-temperature data collected after 20150101 and a recorded Rfree below 25%. All specific contacts between atom-type pairs, where this contact was the minimum (1-4 or 1-5) for a given atom (i.e. assumed to be the one most responsible for determining torsion angle conformation), were used to fit a Gaussian to the resulting histogram using "fityk" by M. Wojdyr. Only pairings with at least 100000 occurrences in the initial database of distances were used to compile a new ideal-contact distance restraints dictionary. (3) Contact distances within aromatic systems are now automatically excluded - since employing 1-4 contact distance restraints e.g. within a PHE, TYR or TRP aromatic ring system is unnecessary and counter-productive. We are aware of several shortcomings of this initial version, although we think it being an improvement on the previous set of restraints. Therefore, we expect further developments both in methodology as well as data harvesting to improve upon this, especially for ligands and other non-amino-acid compounds. For the moment we expect and hope for (a) a smaller number of rotamer outliers that could occur for weak density or where the model moved even out of density, and (b) fewer distortions especially within ring systems. We did run a large number of test cases for comparison that suggest this feature to behave well, but please report any observations (good or bad) back to us - ideally with a detailed description of the chemistry and environment involved. * Major work in handling hydrogens better regarding to: (1) B-factors when using zero-occupancy hydrogens. The B-factors of such hydrogens (or in general: all zero-occupancy atoms) are now detached from the B-factor of the parent (heavy) atom. This avoids cross-talk between atoms where one contributes to the X-ray term and one isn't. (2) Using electron-cloud distances for refinement of full-occupancy hydrogens against X-ray data. All relevant tools and programs have been enhanced to support electron-cloud distances, namely * buster-report, grade, grade_PDB_ligand and hydrogenate (via a "-ecloud" command-line flag) * refine (via the new "-M Ecloud" macro) New versions of restraint dictionaries have been added for the electron-cloud distances, namely: $BDG_home/tnt/data/protgeo_eh99_ecloud.dat $BDG_home/tnt/data/nuclgeo_ecloud.dat $BDG_home/tnt/data/exoticaa_ecloud.dat $BDG_home/tnt/data/cofactor_geo_ecloud.dat * New definition of B-factor restraints (B-correlation) based on the same set of PDB structures as the new contact distance database. This constitutes a much more up-to-date and reliable set of reference values (as well as sigmas) than the small number of original structures the original restraints were based on. The restraint values are now much smaller (sometimes by a factor of 10) and with a much smaller sigma. A typical value would be in the range of +-2 A^2 with a sigma of 3. For that reason, a new default (for bonded atoms without explicit BCORR term in our database) of 0.0 with a sigma of 2.5 is being used #################################################################### ## The above changes result in multiple aspects of refinement being ## modified or improved within the same release. This means that ## various aspects like ideal relative weights between geometry ## terms (including ideal contacts and B-correlation), variable type ## scaling for the minimizer as well as the relative weight between ## X-ray and geometry term might still need fine-tuning. This is ## ongoing work and we expect further adjustments and improvements ## in that area. However, separating the different topics described ## above seemed impossible, since B-correlation, contact distances ## and hydrogen handling are all related and influence each other. #################################################################### * Robustified the determination of so-called "equivalent atoms", i.e. atoms within a residue that are chemically identically but will have different atom names: this now takes better care of different alternate-conformation combinations to determine the maximum number of atoms within a residue (which is relevant to the data structure holding the connectivity information). * Added support for bond types within BUSTER refinement to provide this information to any step or tool that could make use of it. * BUSTER now defines "aromaticity" for a given plane by looking at all bonds within that plane to see if these have a bond type "aromatic". A fraction of more than 50% of these bonds defined as "aromatic" defines this plane to be considered aromatic. * We now compute not only a single, overall rms(bond) deviation, but also intra-residual values for different sets (StdProtein, RnaDna, Buffer and everything else): this allows BUSTER to adjust the X-ray weight based on StdProtein (or RnaDna) values alone to avoid getting biased by a few irrelevant outliers. * Changed default: anomalous as well as F(early)-F(late) difference Fourier maps are now computed by default (if the input MTZ file contains the relevant data items e.g. from autoPROC). This might help characterising anomalously scattering atoms as well as visualising potential radiation damage effects. * New macro to switch to the behaviour of the previous snapshot (as far as possible): adding "-M 20190607" will use the old contact term methodology, B-factor correlation restraints and deactivating automatic anomalous/radiation-damage map computation. * New tool (aB_hydrogenate) to simplify correct hydrogenation of PDB files: * this uses our "hydrogenate" tool (which provides additional control) for the actual hydrogenation via MolProbity's "reduce" program; * it will not only hydrogenate residues as known to "reduce" or as given via the command-line flag (in form of CIF dictionaries), but also attempts to hydrogenate any other existing compoound (cofactors, buffers etc); * two final checks for incorrect handling of alternate conformations (B-factors of added hydrogens are not consistent with associated bonding partner) and hydrogen atom naming for (N-terminal) amino-acids are added: these will also be fixed automatically when using this tool; Please see "aB_hydrogenate -h" for usage help. * Fixed bond-type for aromatic ring systems in nucleic acids ($BDG_home/tnt/data/nuclgeo.dat). * Improvements to the final refine.pdb file: now also writes REMARK 2 and EXPDTA records (thanks to D. Reinert for reporting). * Fixes to ana_pdbmaps to deal with situations where cluster files contain many atoms (thanks to D. Reinert for reporting). * Improvements to internal Gelly algorithm that defines pseudo-chiral centers: take atom type into account as well (to not confuse atoms with/without hydrogens as being identical). Furthermore, we now check for alternate conformation identifiers to only consider atoms that are actually bonded to one another. * Improvements to MTZ files written by BUSTER: this now uses the MTZ dataset hierarchy to include project, crystal and dataset name from the input MTZ file (as well as the cell and wavelength as used within BUSTER). * New jiffy (aB_chiral_volume) to help detecting inversions of pseudo-chiral side-chain centres. * Added a scattering factor entry for S+2. * Update Components-inchikey.ich database to make recognise-compound work for newer compounds. * Fixes to mmCIF reflection data generation: now also include an explicit _refnl.status item (if a test-set flag column is present). * Pipedream: Increased tolerance in comparing cell dimensions of input model and reference mtz file. Changed behaviour if tolerance exceeded from an ERROR resulting in Pipedream termination, to a WARNING message only. * Pipedream: If Rhofit is run, Pipedream will now run post-refinement of what Rhofit considers the "best" solution automatically. For backwards compatibility the -postref option is still defineable, but is no longer required. To turn off post-refinement, the -nopostref option has been added. Improvements and fixes (released Jun 7 2019): * Fixed regression in previous release whereby the automatic adjustment of X-ray weights had been inadvertently made inactive. * Fixes to the DFc completion feature in BUSTER: previous completion was not using the correct coefficients for reflections below the low-resolution limit of the observations, leading to artefacts within the solvent region. Improvements and fixes (released May 29 2019): * Improve the generation of TER records in PDB files. * Robustify treatment of ligands with a highly connected network of bonds. Thanks to Robert Byrne for reporting the issue. * With the update to sftools in CCP4 (7.0.073) there is now broader support for more space groups (especially centro-symmetric ones) in BUSTER. * Added additional check in "fetch_PDB" to handle problematic deposited reflection data (like 6NHD) where some extremely high-resolution reflections are present totally unconnected to the bulk of the data and without having any actual data items (only status and test-set flags). * The automatic X-ray weight adjustment will now only look at the rms(bond) value for standard protein residues (or standard DNA/RNA residues): this should ensure that unusual residues, compounds, buffers or ligands are not dominating the target value - especially if the restraint dictionaries might be less reliable. * A new parameter RmAnisouZeroOccHydrogens (default = "yes") will remove any individual atomic ADP definitions from zero-occupancy hydrogen atoms upon input. * To allow systematic absences being ignored upon input to BUSTER, the new parameter Buster_CadSysAb can be set to "SYSAB_KEEP" (according to the CAD documentation). Thanks to M. Rudolph for suggesting that. * Added new options to Rhofit (-anisofill and -isofill) to use the filled-in 2mFo-DFc map coefficients produced by BUSTER during definition and description (via prep_rhofit and ana_pdbmaps) of the cluster regions to be fitted - instead of the default (map coefficients only for observed reflection data). The anisotropically filled-in version requires the use of a STARANISO analysed dataset within BUSTER - which can come from autoPROC or the STARANISO server. Thanks to Y. Wang for suggesting this. * Improved the handling of command-line arguments to Rhofit by adding more checks in order to catch wrong or mistyped arguments. * Fixed an issue in reporting R/Rfree at the end of standard output from "refine": the values have been out-of-sync with the values given in the tables. * Fixed a problem when running BUSTER with the "-L" ligand detection mode. This could have resulted in leaving waters within the ligand (difference) density as described by the clustering method. * Fixed issue with DFc-completion map coefficients for the highest resolution reflection, which might have had a missing-number-flag (MNF) instead of a valid number. This was due to the limited precision available for reported resolution limits of MTZ files. Thanks to C. Schleberger for reporting. * Fixed typo of F_meas_sigma label for mmCIF file produced by the aB_deposition_tool. * Robustify treatment of unexpected CIF-labels when inserting restraint information with the aB_deposition_tool. * pdbchk_element: fixed issues with names of multiple entries to deal with components.cif as of 20190424. * Fixed renumbering of ANISOU records in hydrogenate for HETATM records with serial number above 9999. * Fixed minor issue in Pipedream of erroneous reporting of resolution limits in summary.out if HDF5 images input. * Corrected Pipedream issue where compressed images input. * Updated Pipedream online help message and manual * Pipedream will write its unique job identification number into Rhofit output Improvements and fixes (released Mar 01 2019): * Added computation of DFc-completion map coefficients in the output MTZ file from BUSTER. The refine.mtz file will now also contain columns (a) 2FOFCWT_aniso-fill PH2FOFCWT_aniso-fill These are 2mFo-DFc map coefficients for all observed and observable (as defined e.g. by STARANISO) reflections. This is based on a column "SA_flag" in the input MTZ file that encodes the classifcation of unmeasured data. These are the coefficients we would recommend when wanting to look at a map with DFc completion. (b) 2FOFCWT_iso-fill PH2FOFCWT_iso-fill These are 2mFo-DFc map coefficients for all reflections up to highest resolution limit of the input data (i.e. within an isotropic sphere). Please be aware that this can lead to serious model bias for very (isotropically) incomplete data (due to anisotropy, missing cusp, ice-rings, detector module gaps etc). These are probably the coefficients required for running e.g. PanDDA (or any other program that requires a full sphere of map coefficients). The columns 2FOFCWT/PH2FOFCWT contain as before the 2mFo-DFc map coefficients for all observed data (i.e. for which a valid amplitude value was provided). We would be very interested in feedback about the advantages or disadvantages of using one or another of those map coefficients: please contact us at buster-develop@globalphasing.com. * Support for generation of a deposition-ready reflection data mmCIF file containing final refinement data - including map coefficients for mFo-DFc difference electron density map as well as 2mFo-DFc electron density maps with different approaches to DFc completion (standard map without completion, isotropic completion to the highest resolution limit of the data and anisotropic completion according to STARANISO analysis of observed/observable reflections). * Added bond-typing to all relevant distributed restraint dictionaries. * Added initial support for electron diffraction (micro-ED) via a set of formfactors and settings - activated by using "-M ElectronDiffraction". Please let us know of any issues (or successes). * Corrected bug in Pipedream when reporting cell dimensions from autoPROC (thanks to P. Rowlands, GSK). Pipedream improvements and fixes (released Feb 14 2019): * Updated the mechanism for running pointless to allow for greater deviation in cell dimensions when checking for consistent indexing against the reference data where Pipedream is run with a pre-processed mtz file. * Corrected a potential problem relating to the column names of F/SIGF data where Pipedream is run with an input mtz file. Thanks to Robert Byrne for bringing this issue to our attention. The naming of F/SIGF columns in input mtz file is no longer defined. Pipedream will now automatically use the first F/SIGF pair encountered in the input mtz file (similar to BUSTER and autoSHARP). If this F/SIGF pair is not the required pair, then Pipedream will need to be run with the -fss option. * Pipedream will generate a unique (uuid-like) job identification number. As well as being written into the summary.out file, it will also be written into both autoPROC and BUSTER standard output files. * In addition to the summary.out file, Pipedream will now output all of the statistics and important run and output information in xml format to summary.xml, to allow easy and automated data harvesting. NOTE: This is the initial release of this functionality and should be considered very much a work in progress at this stage. Both the content and formatting may change in future releases. We are releasing this feature for your evaluation and would appreciate your feedback. * Pipedream will run autoPROC to automatically generate the inlined version of summary.html. It will also no longer generate the summary.tar.gz file. BUSTER improvements and fixes (released Feb 14 2019): * Support for generation of deposition-ready mmCIF files describing the final model, various refinement statistics as well as all non-standard and user-supplied restraint dictionaries. This is controlled via the parameter BusterCreateCif (default = "yes"). This is ongoing work together with the wwPDB PDBx/mmCIF Working Group - for more details see https://www.wwpdb.org/task/mmcif https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files * Improvements to the creation of symbolic links in an attempt to detect filesystems without support for this feature (e.g. some Windows filesystem variants). * The content of the environment variable BUSTER_ReportComment will be reported at the top of standard output (in the section mentioning date, directory, user etc). This allows specification of "context", e.g. if BUSTER is run as part of Pipedream or an inhouse pipeline. * Implemented additional checks to avoid problems in generation of harvest information (going into REMARK 3 record of output PDB file) when running against ultra-low resolution data. Thanks to A. Hruza (Merck) for pointing this out. Pipedream improvements and fixes (released Nov 27 2018): * Updated both pepflip and SideAide binaries. Included new PDB_REDO component, modelcompare. * Updated both pipedream and pepflip-sideaide to run modelcompare if Sideaide (and pepflip) is also run. * Updated Pipedream to remove more temporary files. Also run RhoFit with -scanchiralsboth set by default. * Updated Pipedream to write cell dimensions of reference model and experimental data to summary.out. BUSTER improvements and fixes (released Nov 27 2018) * Update to buster-report to address an issue in the upcoming 2019 release of the CSD. * Upgrade of build system to Intel Compiler version 16 and of optimisation library from PETSc 2.3.2 (with TAO 1.8.2) to PETSc 3.10.2. Several other external packages and libraries have been updated at the same time. Our tests have shown that the resulting binaries perform very similar compared to previous releases, but small differences will occur due to the change in compiler and optimisation toolbox. If you encounter any significant regression, please let us know immediately - ideally with test data so we can reproduce any shortcomings. * Fixed problem in CCP4/PDBSET (by using internal procedure) when handling files from water update procedure. * Additional syntax checks regarding the -RB flag to refine: this should help understand potential error messages better. * Added a -td command-line option to "grade_PDB_ligand": this defines a temporary directory in which all the intermediate files are saved (whereas they would normally be deleted) to facilitate fault analysis. * Added a formfactor entry for B-1. * Update the rvalue tool to do computations on observational scale. This makes the results consistent with those reported from BUSTER. Thanks to Kenton Longenecker for reporting the discrepancy. * Fixed regression in grade-ciftool (as used by RhoFit) regarding the -scanchiralsboth option. * Improved handling of pseudo-chirals in compound dictionaries as used by RhoFit (in conjunction with -scanchiral and -scanchiralsboth): ensuring that those are not kept in list of chirals for scanning. * Updated the hydrogenate script to ensure that the PDB file header added by BUSTER is not truncated at character 80. Added option to ensure that all atoms are numbered sequentially in the output file. Work around to correct issue in reduce if input model is already hydrogenated and contains ANISOU cards, occasionally resulting in orphaned ANISOU cards being left (well spotted by Dirk Reinert). * Updated buster-report to ensure that all ligands are correctly hydrogenated prior to Mogul analysis. This prevents potential incorrect assignment of bond orders by Mogul. Thanks to Thierry Fischmann for reporting the issue. * If refining against the F_early (or F_late) data from autoPROC (via autoBUSTER_FsigF_Pairs="F_early,SIGF_early") we still want to be able to compute the F(early)-F(late) radiation damage detection and visualisation maps: this required a fix in the logic to determine correct columns for these computations. * Better support for multi-dataset structure factor CIF files in "fetch_PDB". * Please note that some applications will be retired in a future release: MDL2TNT MOL22TNT MakePDB MakeTNT PDB2CONF PDB2TNT. It is very unlikely that these were still in actual use, but if you are using these it would be helpful to contact us regarding the feature set they might provide for you. * First release with support for individual atomic anisotropic displacement parameter (ADP) refinement which can easily be activated via the "-M ADP" macro on the command-line. This has been tested on high-resolution structures using data processed by autoPROC and STARANISO. These test datasets - had no completeness issues (e.g. a missing cusp) - showed a clean, single lattice (no split crystals or non-merohedral twinning) - had diffraction limit to 1.2A or higher - used STARANISO data after re-processing the original images with autoPROC The refinements used fully hydrogenated, fully converged and modelled structures with TLS parametrisation. We expect further developments to take place, especially in fine-tuning the different weights and the best refinement protocol when ADP parametrisation is used. We would highly appreciate any feedback about problems or suboptimal behaviour of the current implementation - as well as successful refinements and results. * Fixed handling of atomic type "X" (e.g. in UNX residues deposited in PDB) - to handle them internally consistently as oxygens. Pipedream improvements and fixes (released May 15 2018): * New data plugin mechanism introduced to allow an external script/binary to be used to retrieve information from databases or other sources and use this to provide Pipedream with the identity and location of one or more of the required data inputs. Please see the Pipedream documentation for a detailed description of the requirements for use of this feature. Thanks to Jun Lu for the request. * Minor correction to SideAide script to ensure compatibility with non-BUSTER output PDB files (thanks to Ian Tickle). BUSTER improvements and fixes (released May 15 2018): * The statistics (R, Rfree, completeness etc) for the high-resolution bin as reported in the REMARK 3 section of the output PDB file (refine.pdb) now use equal-observation-number binning similar to autoPROC and STARANISO. This ensures that the values given here are meaningful also for incomplete or anisotropic data. * The rvalue tool now supports equal-observation-number binning (as opposed to equal-volume) via the new '-eqnbin' flag. * Fixed method to move model back to original location if it was far away from the origin. An issue was discovered when the cell parameters in the PDB file differ from the cell parameters from the MTZ file (thanks to Ketan Gajiwala for reporting and providing test data). * Fixed format of proposed LINK cards reported by MakeLINK (thanks to D. Reinert for reporting). * Some code re-organisation to avoid (benign) SC_ARG_MAX warning message in 'refine'. * More improvements when working with hydrogenated models (fully or partially hydrogenated) in combination with occupancy refinement: this should avoid problems in big cycles N>1 when e.g. one alternate conformation gets refined to OCC=0. * Updated the URL of the PDBj repository (to the correct ftp://ftp.pdbj.org/pub/pdb) within 'fetch_PDB' tool. Also: added options -nomerge/-notruncate/-nouniqueify (when used for intensity-only conversions). * The "graph_autobuster_R" tool should now also work for older BUSTER result directories (prior to the "small footprint" work to reduce output size and amount); thanks to S. Sheriff for reporting. * Fixed problem in aB_covalent_ligand when atom names in ligand and protein are duplicated: depending on the order on the LINK card and/or within the PDB file, the final step of adjusting the atom names back to the correct/initial value was not done correctly. Thanks to I. Tickle for triggering that fix. Also added a command-line option to explicitly specify the linkage name used in the resulting dictionary (instead of auto-generating it internally). * When parsing command-line arguments in "refine", detect unsupported formats like "-arg=value" to avoid subsequent failures. Thanks to S. Sheriff for pointing that out. * Improvements to the automatic test for duplicated restraint definitions (which we want to avoid): this should now handle better cases where very similar linkages (e.g. for covalently bound ligands) are described via different residue and/or linkage names. Thanks to I. Tickle for providing examples for this. This check for duplicate bonds can be switched off via the RunBusterRunRemoveDuplicateRestraints parameter (default="yes"). * Within grade (and grade_PDB_ligand): replaced the Perl module POSIX::tmpnam (a security risk) with File::Temp. * The "pdb2occ" tool will now generate Gelly command files, that only automatically exclude hydrogens with OCC=0.0 and not any atom with OCC=0.0. This avoids an error in subsequent big cycles of refinement, when e.g. one alternate conformation is being refined to zero. With this new method such cases should make it correctly into the next big cycle - giving them a chance to have the occupancy refined to a non-zero value in the end. * Better handling of very long (output) directory names, working around filename limitations within the (CCP4) SFTOOLS program. Pipedream improvements and fixes (released Dec 19 2017): * New functionality included to incorporate use of both pepflip and SideAide into the refinement procedure. Please see the Pipedream documentation and Pipedream reference card for a full description. BUSTER improvements and fixes (released Dec 19 2017): * Initial release of programs pepflip and SideAide, part of the PDB_REDO suite, as part of the Global Phasing software suite. With our thanks to Tassos Perrakis, Robbie Joosten and the Netherlands Cancer Institute (NKI). See http://www.cmbi.ru.nl/pdb_redo. * New script, pepflip-sideaide, included in distribution, to allow searching/correction of sidechain rotamers (SideAide) and correction of incorrect peptide backbone flips (pepflip). * New, improved and more consistent handling of hydrogens: - their occupancy will always be set to zero (SetHydrogensOccToZero=yes) within BUSTER itself; - B-factors of hydrogens will be kept fixed (i.e. not refined): SetHydrogensBfixed=yes - on output occupancies will be reset to their input value (SetHydrogensOccToInitial=yes) * Initial release of a utility to help in generation and usage of linkage restraints dictionaries when encountering covalently bound ligands: aB_covalent_ligand. Documentation and detailed example usage is provided within the online manual ($BDG_home/docs/autobuster/manual/autoBUSTER7.html#aB_covalent_ligand). We hope this to be useful for simple and straightforward situations, but expect issues in more complicated cases (alternate conformations, non-unique atom naming, poor initial geometry for linkage ... ). Any feedback about performance, failures (and successes!) would be highly welcome - in order to improve the tool as well as the general approach taken within BUSTER ("refine") and to gather more realistic, real-life examples of typical covalent linkages. * Added automatic support to FREER as test-set flag column names (since CCP4i2 seems to use this). * Improvements to "pdb2occ" tool (to generate definitions of occupancy refinement groups and restraints): - by default this now ignores hydrogens (set parameter Pdb2OccUseHydrogens to "yes" in order to include them); - ensure we only have a single OCCSUM restraint per alternate-conformation refinement group; - atoms with zero occupancy are excluded from occupancy refinement; * When initial sanity check fails due to missing SSBOND cards: actually show the suggested cards to make it easier to cut-n-paste those into the starting PDB file. * pdbchk_element: fixed issues with names in 4EX and 9YP to deal with components.cif as of 20171208. * Fix to Grade reading an SDF file with more than 99 bonds. Thanks to Gabor Bunkoczi for reporting and providing an example. Pipedream improvements and fixes (released Sep 20 2017): * Pipedream will now run automatically with an input mtz file containing more than one set of structure factor amplitudes. It will default to using F/SIGF, followed by FP/SIGFP. Only if neither set are present will Pipedream terminate. BUSTER improvements and fixes (released Sep 20 2017): * Considerably reduced the amount of files and data written during a 'refine' job: this can reduce the disk space occupied by about 80%. * Added low-level utilities (aB_pdb_1and2, aB_pdb_1close2, aB_pdb_1not2, aB_pdb_select and aB_remove_duplicate_restraints). * pdb2tls: minor change to make it run using mawk. Thanks to Boaz Shaanan for reporting the issue. * Updated primary protein restraint dictionary (protgeo_eh99.dat), replacing TRIG restraints with PLANE restraints. This is in response to reports about problems with planar side-chain showing non-planarity after refinement with BUSTER. * Hydrogenate utility updated. Hydrogen atoms will be placed based on nuclear x-H distances, rather than electron cloud based distances. The -zero option has been removed. All hydrogens will be added at zero occupancy by default. * When encountering highly unusual MTZ files that cause problems in the early stages of running 'refine' (i.e. the MTZANA call to extract per-column resolution limits), we now report this as a warning and don't stop with an error. * Update to both grade and grade_PDB_ligand. Neither will run if CSD/Mogul is not available and properly defined, unless the -nomogul keyword has been specified. Use of -nomogul is not recommended and will result in a specific warning message about its use and dictionary quality. The -nomogul option is deprecated and will be removed completely from a future release. * Fixed inconsistency in Mogul analysis at the Grade (dictionary generation) and buster-report (ligand analysis) stages: these should now be consistent. * Added options to RhoFit to only scan chirals that are marked as "both" in the dictionary ("-scanchiralsboth") or to only scan specific chiral(s) ("-scanchiral "). See "rhofit -h" for more details. Pipedream improvements and fixes (released June 20 2017): * Output appropriate summary of autoPROC processing statistics in summary.out depending on whether or not anisotropically analysed (Staraniso) output file is used in subsequent steps * If run with raw images as input, run BUSTER with AutomaticFormfactorCorrection=yes defined. * Allow input of compressed images (-allowcompressedimages option) BUSTER improvements and fixes (released June 20 2017): * pdbchk_element: fixed issues with names in 6KB, 8WV and OEY to deal with components.cif as of 20170531. Pipedream improvements and fixes (released May 05 2017): * If input experimental data is an mtz file, run mtzchk to ensure consistency. Thanks to Paul Rowlands for reporting an issue. BUSTER improvements and fixes (released May 05 2017): * Better handling of single-atom residues - including HOH and NH2 - when describing the structure via the TNT sequence file. * Fix an issue for very short cell axis where in some cases the refinement would stall. Thanks to Michael Sawaya for reporting the issue. * Update installation guides for CentOS-distributions. Thanks to Wei-Chun Kao for reporting some suggestions. * Fix to buster-report to allow special characters in SMILES. Thanks to Wei-Chun Kao for reporting the issue. * pdbchk_element: fixed issues with names in ZN7, ZN9, K8P, 7WJ and 86M to deal with components.cif as of 20170217. * rvalue: new option "-g" to compute generalised R-values. Suggested by Dirk Kostrewa. * Update documentation for MakeLINK. * Fix to fetch_PDB when running with -nosf and the same identifier multiple times (reported by D. Reinert). * Fix to grade-ciftool such that CIF file from jLigand can be read without needing manual editing. BUSTER improvements and fixes (released Dec 07 2016): * Prettify output of grade_PDB_ligand. * Fixed regressions in REMARK 3 records of output PDB file (reported by S. Sheriff): - items that should have been reported as 'NULL' were given as "0.0" instead; - precision of high-resolution bin R-values should have been 4 digits; * Added possibility to provide own REMARK 3 header template by setting parameter autoBUSTER_Remark3HeaderTemplate (see the default file $BDG_home/database/files/Harvest/header.pdb as an example). * Improvements in graph_autobuster_recipCC utility (use same ice-ring locations as in autoPROC and honor range of CC values when plotting those). * Fixed regression during water addition (when ignoring hydrogens): this resulted in hydrogens with OCC=0.0 getting deleted completely (reported by S. Sheriff). * Introduced possibility to keep all waters present in input file untouched by our own water-update procedure by setting parameter WaterUpdateKeepExisting to "yes" (default is "no"). This has no effect when using other water-update procedures (like ARP/wARP, Coot's findwater or your own tools). * When running "refine" with "-L" option: also report how many (potentially) "interesting regions" were found. * Added flag -chirality-both to both the "grade" as well as the "mol2_to_cif" tool (which is called by Grade): this will set any chiral center to 'both' (instead of computing this as 'positive' or 'negative' depending on input coordinates). Since MOL2 files don't specify stereochemistry explicitely but only through the 3D coordinates (which can be of dubious or undefined origin), this allows users to override the current behaviour (reported by M. Mathieu). * During PDB checking (with 'pdbchk') of missing atoms that are referenced in other records, we now ignore waters - ie they still give a warning but will not trigger an error. This is relevant for re-refinements of deposited PDB structures when water-update is involved: PDB entries can contain some very bizarr LINK records involving HOH residues. * pdb2occ now allows generating BUSTER_OCCSUM instructions also for more than 2 alternate conformations: the parameter Pdb2OccMaxAlt (default=2) can be increased to restrain multiple conformations to have a summed occupancy of one. * Added documentation about the ATOMTYPE property in Gelly selection syntax (see $BDG_home/docs/gelly/manual/gelly2.html). * Multiple changes in Gelly to improve numerical stability, error handling and memory management. Also: * added analysis of bond type within rings (allows classification of a ring as being aromatic or not); * by default RhoFit will not randomize dihedral angles around aromatic bonds now; * in Grade context: instead of resetting all coordinates to (0,0,0) when generating a model based on a restraints file, we now start from the coordinates as given in the input restraints file; * Improved H-placement within 'hydrogenate' by switching off the check in 'reduce' that hydrogens should not bump into non-metal atoms: this might make sense in the "molprobity" context, but 'hydrogenate' should not second-guess here. After all, the resulting (hydrogenated) model is usually then given to BUSTER for refinement, where any bad contact would probably be removed anyway. (Reported by D. Reinert). * Robustify location of temporary files for bulk solvent generation. * added more high-resolution ice-ring markers to graph_autoBUSTER_recipCC utility: 1.52, 1.47, 1.44, 1.37, 1.36, 1.30, 1.27, 1.26, 1.22, 1.17 and 1.12 A. These are based on high-resolution datasets (with ice-rings) and comparison to [1]. [1] Kumai, M. (1967). A study of hexagonal and cubic ice at low temperatures. Research Report 231, U.S. Army Materiel Command, Cold Regions Research & Engineering Laboratory, Hanover, NH. BUSTER improvements and fixes (released Sep 30 2016): * Fixed a regression (released Jul 6 2016) that made Gelly erroneously generate 'special position' EXCLUDE cards for Grade runs. Pipedream improvements and fixes (released Sep 23 2016): * Added -h5master input option to allow Pipedream to run with input Eiger HDF5 data. BUSTER improvements and fixes (released Sep 23 2016): * Fixed water addition procedure to ignore existing hydrogen atoms. * Updates to PTR (O-PHOSPHOTYROSINE) restraints (reported by P. Rowland). * pdbchk_element: Fixed problems for atoms named NP and corrected the logic to make option '-c' work again to produce the chemical composition. Also update to handle components.cif as of 20160824 and consolidated internal coordinate conversion. * Increase the number of possible refinement notes in output PDB file to cater for structures with many ligands treated with QM. * Corrected some typos/units/links in the output from buster-report. * Make it possible to run multiple concurrent instances of buster-report sharing the same current directory. * Fixed problem with buster-report PDF generation when BCORR (B-factor correlation restraints) outliers are to be reported: this lead to a pdflatex failure (reported by S. Sheriff). * gelly_refine: use known location of BUSTER programs instead of relying on $PATH. This prevents Grade from failing due to external packages having eg. a pdb2seq program installed in /usr/bin. Pipedream improvements and fixes (released Jul 08 2016): * Fixed regression when starting from diffraction images introduced in the latest snapshot (due to changed autoPROC defaults): avoid stopping with error when F_early/F_late amplitudes are being found in autoPROC output MTZ file. BUSTER improvements and fixes (released Jul 08 2016): * When requesting the computation (and analysis) of anomalous Fourier maps (BusterAnoFourier=yes) and/or F(early)-F(late) difference Fourier maps (BusterEarlyLate=yes), the reflection data will be included into the final "refine.mtz" file by default - if the input MTZ file contained the appropriate columns. If this is not wanted the parameters BusterAnoFourierIncludeInFinalMtz and BusterEarlyLateIncludeInFinalMtz could be set to "no". This useful feature was suggested by D. Reinert. Pipedream improvements (released Jul 06 2016): * added "-useaniso" command line option to instruct Pipedream to use the anisotropy correct output from Staraniso in place of the standard output from autoPROC for subsequent steps. This option is only applicable where raw images are input for processing with autoPROC. BUSTER improvements and fixes (released Jul 06 2016): * Fixed issues in Grade/Gelly where 3-rings were incorrectly setup as torsion restraints. * Fixed issue in Gelly where atom names that are four characters wide and have an alternate location indicator could give incorrect diagnostics in the sanity-check. * Improved handling of close contacts across symmetry elements (i.e. atoms/residues on special positions): * The new default is to only auto-generate EXCLUDE cards if the contact across symmetry involves atoms from the same residue. The previous behaviour will generate EXCLUDE cards also for different residues that are in close contact across a symmetry element. This old behaviour can be reinstated by using the new flag "-special_all" if absolutely necessary. * Modified the default distance for atoms/residues close to special positions from 0.5A to 1.5A (unless -special_all is set in which case it stays at 0.5A). This is required for the new approach. * The logic for auto-generating EXCLUDE cards has been improved: we now detect contacts across symmetry between any atom of residue X to any atom of residue Y. The previous requirement (atom in close contact to itself across symmetry) would only detect single atom residues or require that at least one atom points close to the symmetry element. However, larger molecules can stay far away from the symmetry element while at the same time overlap a lot (see for example 5BQX). * Within a BUSTER refinement, any auto-generated EXCLUDE card is put aside after big cycle 1 and this list used for all following cycles. This ensures that the handling of residues/atoms close to special positions stays consistent throughout a BUSTER refinement run (previously, the EXCLUDE list would have been generated afresh at each big cycle, leading to the sudden introduction of bad contacts within a BUSTER refinement due to very small shifts and therefore pushing residues/atoms close to special positions out of density in the resulting model). BUSTER improvements and fixes (released May 01 2016): * new options to "rvalue" tool (for computing R-values after BUSTER refinement) to have complete control over the binning used in computations. This enables identical binning even for BUSTER refinement results at different resolutions. * fixed two issues in "covalent_grade_create_linkdic.pl" tool regarding automatic detection of atom names of covalently linked residue portion. See also BUSTER wiki page at https://www.globalphasing.com/buster/wiki/index.cgi?GradeCovalentTutorial * pdbchk_element: update to handle components.cif as of 20160411. =================================================================== Changes included in BUSTER version 2.10.2 stable Mar 24 2016 =================================================================== BUSTER improvements and fixes (released Mar 24 2016): * Added a feature to pdb2occ that allows explicit specification of residues by type (3-letter residue name) or identifier (chain name and residue number). This simplifies the generation of Gelly command files for occupancy refinement of compounds and ligands. See documentation and out of running "pdb2occ -h" for more details. BUSTER improvements and fixes (released Mar 02 2016): * Instead of only warning about a model being too far away from the origin (often resulting in a failure later), the pdbchk step will now also correct for this. By default the required shift will be undone at the end of refinement so that the output PDB file will have the same position as the input model. * During refinement, the same set of automatically determined EXCLUDE cards is now used throughout the refinement. These are determined during big-cycle 1 to avoid bad contact terms between atoms across symmetry elements. By re-using the same set throughout we avoid that a shift in coordinates - to accommodate electron density features - could result in an initially excluded contact term to suddenly becoming active (which could result in a sudden movement at a later big-cycle). Pipedream improvements (released Feb 25 2016): * By default, the post-refinement step will refine the occupancy of ligands fitted by RhoFit. * Added -nooccref command line option to tell post-refinement not to refine ligand occupancy * Added -postthorough option. Tells Pipedream to perform a more thorough post-refinement, involving two BUSTER runs. * Added -nobr option to instruct Pipedream to not run buster-report * Updated Phaser version warning message for new version of Phaser in CCP4 7.0 * Improvements to ERROR reporting BUSTER improvements and fixes (released Feb 25 2016): * pdbchk_element: update to handle components.cif as of 20160112. * fetch_PDB: take care of structure-factor CIF files where the _diffrn_radiation_wavelength loop might also contain a weight (.wt) item: see eg 5ewn. BUSTER improvements and fixes (released Dec 14 2015): * Major reworking of geometry checks, including the initial sanity check: * When encountering atoms without bonds, some additional analysis is done to help users when this occurs for known/standard residues. * Re-organisation of the initial sanity check routine - keeping the underlying logic, but * tidied up formatting of messages; * adding an identifier (check-NNN) to each check - visible only in the detailed gelly_sanity_test.log file and not in the shortened gelly_sanity_test.lis version. This helps communication with developers but also detecting common patterns or problems. * sanity check is now aware of Buffer, RNA/DNA, Metal and Sugar residues; this allows much finer control of what message to produce; The biggest impact on reducing the number of close contacts often wrongly classified as errors is due to a second check once such a close contact is detected. Instead of assuming anything closer than an ideal contact is most likely a covalent bond we now analyse the distance of those two atoms (knowing their atomic type) against ranges of known covalent distances for those two atom types. If the distance is within -0.1/+0.1 A of that range we will still give an ERROR, but if it is only within -0.5/+0.5 we now give a WARNING. Anything further away is only reported. * Added support to compute and analyse anomalous Fourier maps (if anomalous differences are present in input MTZ file). This can be switched on with BusterAnoFourier=yes (default-no) and maps can be kept on disk with BusterAnoFourierKeepMap=yes (default is to keep only the analysis while removing the map file). * Added support for calculation and (optional) analysis of an F(early)-F(late) difference Fourier map: * this can be selected with BusterEarlyLate=yes (default=no) and results in a MTZ file (refine_early-late.mtz) containing columns F_early-late/PHI_early-late for computation of such a map e.g. within Coot. * to perform some automatic analysis, the BusterEarlyLateAnalyse parameter can be set (default = same value as BusterEarlyLate); * When counting non-hydrogen atoms for the REMARK 3 header, count alternate conformations only once (reported by S. Sheriff). * Fixed dictionary for HEC heme. * Added modified RNA as defined at http://modomics.genesilico.pl/ (Machnicka, MA et al (2013). Nucleic Acids Res 41, D262.) if they occur in at least 10 PDB entries (as of 20151110) to list of known nucleotides MakeLINK should recognise as being covalently connected. * Fix in visualise-geometry-coot: added support for contacts across symmetry in order to give correct residue name and text in contact tab. * Some cleanup in files like LIST.html, gelly_sanity_test.log or screen_final.txt: * To avoid excessively verbose logfiles (especially for large structures), a default number of the first 100 items is now reported. For debugging purposes this parameter can be changed via the -report_numtop flag. * Some small format changes for better readability throughout. * Speedup at different stages, especially noticeable with very large structures. * Added check for PDB-style symmetry operators: if these don't fit the format NNNMMM it is most likely due to molecules being positioned very far away from the (0,0,0) origin. * Some additional consolidation in the REMARK 3 section written (follow closer the more common formatting seen in deposited PDB files). BUSTER improvements and fixes (released Nov 25 2015): * pdb2occ now reports the correct number of atoms within an altConf-based group in the comment. * Added N (generic RNA nucleotide) in order for MakeLINK to create correct linkage when encountering this residue. * Ensure our REMARK 3 records are following the most common formatting regarding text and precision of numerical values as present in deposited PDB files. Please note that for most sections of the REMARK 3 record investigated, no a single format and precision was seen after analysing all deposited X-ray PDB structures as of July 2015. The user can adjust the required precision for each numerical (floating point) value by (a) finding the parameter name (__SOMETHING__) in $BDG_home/database/files/Harvest/header.pdb (b) setting the parameter autoBUSTER_Remark3Precision_SOMETHING to the number of significant digits one wants; e.g. refine autoBUSTER_Remark3Precision_RFREE=4 ... would change it from the default of 3 and ensure that the overall Rfree is printed as 0.2133 instead of 0.213. * Fixed problem in counting the number of hetero atoms for the REMARK 3 record (thanks to S. Sheriff for pointing this out). * Fixed problem in Grade: it generated too many unnecessary pseudochirals when using MOL2 files (reported by Y. Wang). Pipedream improvements (released Nov 25 2015): * Changes to limited MR module required to ensure compatibility with Phaser 2.6.0 and CCP4 7.0. These changes have no impact on function and are backward-compatible with earlier versions of Phaser (back to version 2.5.6). * NOTE: The result of this update effectively means that the minimum version of CCP4 required by BUSTER increases from 6.3 to 6.4. BUSTER improvements (released Sep 23 2015): * Fixed bug in MakeLINK regarding symmetry description on SSBOND cards: now use full width of 6 characters (instead of only 4) as defined in http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#SSBOND. * Improved MakeLINK to avoid error about (unsupported) TAB characters in PDB file records that are actually not used within MakeLINK. buster-report improvements (released Aug 12 2015): * PDF page produced now has the same ligand information as the HTML version, including electron density picture and Mogul outliers 2D schematics and tables. * report.xml now contains all the numerical information about each ligand including Mogul outliers. * New option (-EDcontours) to set the contour levels used in the electron density around the ligand pictures. * Improve the captions for Mogul schematics by getting rid of the colored text previously used: instead describe the colors. * Ligand pages now have help hyperlinks in each section. These link to the relevant part of much improved BUSTER wiki help page. * Support for ligand corporate ID's improved with option to allow multiple ligand corporate id substitution patterns. The documentation for this feature has been much improved. * Improved the directory structure and filenames used for ligands. * Corrected bug where empty ligand pages could be produced for structures containing no ligands but monoatomic ions. * Improved the list of "boring" ligands. * Corrected bug where multiple simultaneous buster-report runs could interfere with one another by using the same temporary filenames. * Numerous other bug fixes. BUSTER improvements (released Aug 12 2015): * added modified amino-acid residues ALY (N(6)-acetyl-L-lysine, 132 PDB entries) and M3L (N-trimethyl-L-lysine, 167 PDB entries) to list of automatically recognised peptide-linkages. BUSTER improvements (released Jul 15 2015): * pdbchk_element: update to handle components.cif as of 20150626. * Added support for AddMissingSsbondRecords parameter to recover lost SSBOND records at the beginning of refinement: * Until now, as we were using MakeLINK by default for the generation of the TNT-sequence file, setting this parameter to "yes" had no effect unless "pdb2seq" had been chosen as an alternative to MakeLINK (by setting SequenceFileGeneration=pdb2seq). * This has now been changed (in response to popular demand) so that specifying AddMissingSsbondRecords=yes will automatically generate SSBOND cards for cysteine disulphide bridges that are (1) missing in the PDB file header and (2) supported by the geometry in the input model (with respect to bond distances, bond and torsion angles). This is intended for situations where e.g. a PDB model was refined with correct SSBOND records but subsequently processed in such a way that the relevant SSBOND records got lost (e.g. stripped by a MR program or step). This option is not intended as a method for inferring the possibility of generic disulfide linkages where the relevant geometry is too far away from ideal. * Setting AddMissingSsbondRecords=yes (the default is still "no") will activate the PdbChk_MissingSsbond check within 'pdbchk' (which is off by default). * The 'pdbchk' step will then use the new 'ana_ssbond' tool to check for missing SSBOND records, using bond distance, bond and torsion angles as criteria. The default criteria are based on an analysis of 28389 SSBOND records in 3906 PDB entries and use min/max values that contain at least 98% (99% for angle) of all deposited SSBOND records: CYS-SG ... SG-CYS distance : 1.948 ... 2.153 A CYS-CB-SG ... SG-CYS angle : 91.743 ... 117.406 degree CYS-CB-SG ... SG-CB-CYS torsion-1 : -130.243 ... -45.321 degree torsion-2 : 33.914 ... 154.916 degree * The presence of ZN or FE atoms close to CYS-SG atoms (3A cutoff) will exclude those CYS residues from further analysis. * Tests have shown that for well-refined structures, all SSBOND records are recovered in about 70% of cases. * Known issues: * CYS-CYS disulfide bonds across symmetry elements are not detected (we are working on this); * non-CYS disulfide bonds are not supported; * alternate conformations can cause SSBOND records to not be detected (we are working on this); * Fixed problem on OS X (10.7 and later): pdb2tls used an unsupported awk construct that resulted in failure to extract existing TLS descriptions from PDB file header. * Fixed problem when running 'refine' with an input TNT sequence file (-Seq argument): if this contained a CHAIN specification for a chain that had no atoms in the PDB file, the automatic generation of RB descriptions (-RB flag) was causing failure within BUSTER. Pipedream update (released Jul 15 2015): * Write "Pipedream" header to the top of the final output pdb file indicating the identity of the input pdb file on which the final output is based. Where Pipedream has been run with multiple input models, it will indicate which of the input models was selected as the best and used for full refinement and ligand fitting. * Renamed -seq option to -sequence to prevent ambiguity with -seqin options. Pipedream update (released Jun 16 2015): * corrected a bug that may affect the correct selection of the best input model where run with multiple input models. BUSTER improvements (released Jun 16 2015): * allow more control about geometry analysis (screening) inside BUSTER via the RunScreenInsideBuster parameter (default=yes) * removed -f flag (we did warn about this being deprecated): it had no meaning/function any longer * reporting of OS information now avoids duplication * handle ColumnName_FreeR_flag_allowed settings that don't follow the required formatting and automatically adjust for that * add check for correct syntax of autoBUSTER_hls setting - and also allow comma-separated list * 'rvalue' tool: widening of output format (for reflection numbers) to allow very large datasets like ribosomes to give correct formatting * added option -nostop to fetch_PDB tool: don't stop if a problem is encountered (like a missing reflection data file) General improvements and changes (released Mar 16 2015): * The need to obtain a separate licence key for each machine on which the software is to be run has been removed for academic users: a single valid licence key will now work on any number of machines. Pipedream updates (released Mar 16 2015): * restricted resolution range for rigid-body refinement to 9.0 - 4.0 A. This change increases the radius of convergence for the rigid-body refinement step and also increases its speed (confirmed testing on multiple test sets, including all of the Pipedream tutorials). * Corrected bug whereby post-refinement would fail in cases where Pipedream is run in "cocktail" mode (multiple input ligands for RhoFit), and several ligands have the same residue name (three-letter code). * All messages output where Pipedream terminates with an error status are prefixed with ERROR: * Corrected bug whereby Pipedream would fail if reading input model from a read-only file system * Corrected potential undefined variable warning that may have occured when running the check indexing function. * NEW FEATURE: Pipedream can now be run with multiple input models. Several input models of the same target (same space group and cell) can be specified. Pipedream will analyse all of the input models against the experimental data and then select the model that best matches the input data by a variety of criteria. Please see the Pipedream documentation and also Pipedream tutorials on the BUSTER Wiki for a full description of the use and limitations of Pipedream with multiple models. BUSTER improvements (released Mar 16 2015): * Set fixed y-range for FOM-plots. * Extend the allowed range for a free flag value to [0-999]. * pdbchk_element: update to handle components.cif as of 20150227. * fetch_PDB: additional tests and checks to ensure the correct wavelength is put into the MTZ file. Also: - report a missing reflection file more explicitly - added warnings for weights below 0 or above 1 and phases below -360, above +360 or more than 360 degrees apart * Allow an alternative way of calculating Luzzati coordinate error estimate with the new tool 'luzzati'. This should be more accurate than the CCP4 program SFCHECK (since it uses the FC values directly out of BUSTER) and is also significantly faster. To switch back to using SFCHECK: please add the 'RunSfcheck=yes' parameter. * Changed default name of buster-report output directory to contain '-' instead of '.' (but user can override this via the BusterReportDirDelim parameter, which defaults to '-'). * Added method to ensure that some user-supplied residue names are output as HETATM and not ATOM (eg. if ligand is amino-acid): this requires the user to set the EnforceHetatmForResidues parameter to a (space-separated) list o chain and residue numbers (eg. "A301 B301"). * Added reporting of resolution limits also for each normal big cycle (not only for rigid-body cycles). * Improvements to reporting restraint dictionary details to output PDB and buster-report. * Updated distributed ANP and NAD restraint dictionaries. * Accept also DCY on SSBOND records in PDB files. BUSTER fixes (released Mar 16 2015): * Handle water update correctly if removed waters are part of a TLS group (and therefore contain also an ANISOU card in the PDB file). * Added check in 'diff_fourier' when comparing peaks against existing PDB file. * Fixed counting of hetero-atoms for REMARK 3 section when no hetero-atoms are present. * Fixed help message (to follow documentation, ie. including -report at the -h level). * Better checks regarding amplitude/sigma (F/Q) pairs in MTZ file (error out if no complete F/Q pairing could be found). Pipedream update (released Jul 26 2014): * Modified default resolution limits to use for the limited MR step. Only restrict high res limit to 3A and do not apply a low resolution cutoff. This bypasses a potential Phaser problem if the lowest resolution bin does not contain any reflections. * Improved and expanded on the termination messages generated in case of a Phaser failure. BUSTER improvements (released Jul 26 2014): * Restraint dictionaries for common sugars are now supplied as cif format files in common-compounds. Restraints for additional sugars also supplied. New restraints included for additional glycoprotein and polysaccharide links. * the 'fetch_PDB' utility now reports any PDB identifier which is skipped because the output directory (and files) already exist. It also reports the location (local directory or remote URL) from where the DB files were retrieved from. * added checks for sensible values to the -nbig/-nsmall command-line options for 'refine'. buster-report and Grade improvements (released Jul 26 2014): * Improved colors used in buster-report ligand Analysis page to be useful for color-blind users (and clearer for everyone). * Introduced support for ligand database/corporate ids. Use the new Grade option -databaseid. The corporate ID will then be prominently displayed on the buster-report Ligand Analysis Page. Furthermore it is possible for the corporate ID to hyperlink to a relevant intranet or external web page. Correction (released Jun 20 2014): * added updated sugar restraint dictionary that was left out in the Jun 12 2014 release. Distribution fixes (released Jun 19 2014): * added two missing tools that where only documented but accidentally left out of the distribution: 'diff_fourier' and 'ana_diffmap_residue'. MakeTNT fix (released Jun 12 2014): * Corrected problem that prevented MakeTNT running under OSX. Pipedream updates (released Jun 12 2014): * Changed the minimum required version of Phaser to 2.5.0 from 2.2. This change will also have the effect of requiring a minimum CCP4 version of 6.3.0. * Added compatability checks to confirm that the binary architecture of the configured autoPROC and/or BUSTER binaries matches the architecture of the host OS. Pipedream will terminate with an appropriate message should the program and machine architectures differ. * Added verbose (-v) command line option. If selected, Pipedream will report its progress to standard output. BUSTER improvements (released Jun 12 2014): * Improved description of nomenclature used to describe sugar linkages in the supplied sugar restraint dictionary (sugar.dat) and the linkage description file (connectAt.dat). * Added restraints for sugar beta-L-fucose (FUL) to sugar.dat and added to linkage description file. ------------------------------------------------------------------- <-- Below are the Release Notes for the previous stable release --> ------------------------------------------------------------------- =================================================================== Changes included in BUSTER version 2.10.1 stable May 12 2014 =================================================================== #### Improvements to make BUSTER package easier to install/test: * comprehensive "follow me" installation instructions showing how to install, configure and test BUSTER on all major operating systems. These are available from the download page on www.globalphasing.com or included in each installation as $BDG_home/docs/installation/index.html * Environment variables can now be used to specify the location of external helper tools for buster-report, grade, grade_PDB_ligand and hydrogenate. Alternatively the tools will be located from the user's PATH. Environment variables can also be set to "none" to indicate that a particular tool is not available, and to turn off its use. * checkdeps tool: this script runs a series of checks that all the required and optional external helper tools work properly. It is designed so that a busy systems manager can quickly check that all BUSTER tools will work properly on a particular host. #### RhoFit now included in the academic BUSTER package: RhoFit is a tool for fitting ligands into difference density. It is able to change bond lengths and angles within the ligand, as well as rotate torsion angles, allowing it to search for correct ring conformations, including macrocycles. In addition, RhoFit can also search for the correct chirality, if not known, for an input ligand (and the density is good enough). RhoFit uses the Gelly geometry function to assess ligand strain and protein-ligand contacts, so its results will be compatible with further BUSTER refinement. RhoFit is designed to work well with BUSTER options for improving ligand density (-L). To help in visualizing results, we provide a tool visualise-rhofit-coot to use coot to quickly inspect the hits generated. RhoFit was originally released to Consortium users in Nov 2009. It is included as part of the academic BUSTER package from May 2014. #### buster-report now included in the academic BUSTER package. buster-report is a tool that provides clear, short reports of how a BUSTER run has proceeded, and an analysis of the final results including ligand geometry assessment from Mogul and protein geometry analysis using Molprobity. Please see: http://www.globalphasing.com/buster/wiki/index.cgi?BusterReport for more information on buster-report. buster-report was originally released to Consortium users in Dec 2011. It is included as part of the academic BUSTER package from May 2014. #### Pipedream now included in the academic BUSTER package. Pipedream is a tool designed to facilitate the use and integration of automated data processing with autoPROC (where installed), structure refinement with BUSTER together with (where requested) automated ligand fitting with RhoFit and buster-report into a high-throughput fragment/ligand screening pathway. Pipedream was developed as part of the SILVER project www.silver-europe.com (FP7-HEALTH-260644) for academic partners. It has subsequently been successfully adopted by a number of Consortium users. It was initially released in Aug 2011. Pipedream is included as part of the academic BUSTER package from May 2014. #### BUSTER. Improvements: * switch to using PDB v3 atom names in all tools. * Extension to the use of the -qm method for representation of ligand geometry using a quantum chemical method to allow use of GAMESS, Gaussian or MOPAC2009 programs. See http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQMhelpers * -forcefield option. This provides for using the force field to represent a ligand. The initial release supports use of the helper program provided by OpenEye (http://www.eyesopen.com/) for MMFF94s: See http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandForcefield * new options to 'refine' command: [[-report|-reportrm] [] to run "buster-report" at end of refinement and, optionally, remove original subdirectory. * Change to the number of threads that refine will use by default (nthreads). This is now set by finding ncpu (the number of CPUs that the operating system reports). The value of nthreads is set to min(ncpu,4) if ncpu < 24, 6 if 23 < ncpu < 63, 8 otherwise. The default can be overriden by environment variable OMP_NUM_THREADS or by refine command line argument -nthreads. See BUSTER documentation $BDG_home/docs/autobuster/manual/autoBUSTER4.html#refine_default_nthreads for full details. * Allow refinement of larger structures. Increased the maximum number of atoms from 520000 to 640000. Note: this doesn't add the capability of using split PDB files to BUSTER! It is still necessary to combine such split PDB entries into a single PDB file (taking care to preserve NCS if present etc) before running 'refine'. * visualise-geometry-coot now loads up the restraint dictionaries which have been cached by autoBUSTER. * better handling of residues with insertion codes in visualise-geometry-coot * alter geometry function to prevent unrealistic short contacts between atoms involved in hydrogen acceptor-donor bond contacts. * alter geometry function to restrain chiral atoms that flatten earlier. This results in MolProbity reporting fewer C beta deviations and fewer REMARK 500 exceptions being listed for BUSTER refined structures. * pdb2tls: - improve error-detection and conversion of TLS group info - robustify interpretation of TLS selection records * pdbchk: check (and possibly correct) that - atom names are in uppercase - residue names are right-adjusted - there are no bogus oxygen charges for ASP and GLU * pdbchk_element: - update to components.cif as of 20140131 - detect and correct if element type is in lowercase * use TNT contacts for metal atoms in ligands containing supplied as .cif dictionary as these are checked and corrected. * alter range interpretation specification such as NOTE BUSTER_COMBINE XYZ { A|100 - A|200 } to not require that residue 100 is present in the file but instead be purely numeric. * extend utility distance restraints to be able to work on the distance between an atom and an atom across a crystallographic contact. This is particularly useful to prevent atoms on special positions or axes from drifting from the position/axis during refinement. * MakeLINK directives can now be added to TNT dictionaries for links so that the restraints can be automatically processed by refine -l. See http://www.globalphasing.com/buster/wiki/index.cgi?GradeCovalentTutorial * increase limit of reflection indices from 255 to 511. * improve reproducibility of the openMP-section of the scaling module (ALABASTER) when using more than two threads. * Update the NotHET set with PDB version 3 names for DNA such that a correct ATOM record (rather than a HETATM record, as previously) is written to the final refine.pdb file. Thanks to Mike Swan for reporting this. * samples/autobuster/refine_test.sh: this test script now reports SUCCESS or FAILURE. In addition the argument -nthreads can now be supplied. * added column names "FreeRflag" and "R-free-flags" to automatically recognized list of allowed test-set flags in the input MTZ file. * automatically insert into list of allowed test-set flags the one specified using command line option: ColumnName_FreeR_flag. * improve handling of what SFTOOLS thinks is an XPLOR RFREE column. * harvest: speedup the processing of REMARK records * new tool 'rvalue' to compute R-values of final mtz file at specified resolution range. R-values can be based on either Fc or Fx. * new tool 'fetch_PDB' included. This script will fetch both coordinates and reflection data from a local or online PDB archive (and convert the reflection data to MTZ format). Fixes: * fix bug that caused refine crash when temperature factor restraints for a similarity group are combined with the -autoncs_weight command. * fix memory access bug that caused refine to issue PETSC warnings and occasional crash when using -qm option to refine ligands using a quantum chemical representation. * during water-update: an error was triggered (wrongly) if initially added waters were completely removed in a subsequent stage - added check for this. * slight change in logic for excluding duplicate restraints (to avoid having same restraints in both the residue dictionary as well as the linkage dictionary). This should get rid of a few failures with 'something wrong when excluding XYZ restraint from ...' messages. * pickup any TLS-parameters after doing a rigid-body cycle. Thanks to Dirk Kostrewa for reporting this issue. * when all atoms of all instances of a specific residue name in the PDB file had their occupancy set to zero, 'refine' would stop with an error about getting the best residue. This has been reset to also allow residues with zero occupancy to be used for testing consistency between the input PDB file and any dictionary (user-supplied or distributed). * fixup precision of resolution range to avoid losing reflections. * eliminated some warnings going to stdout when running from perl. * regain openMP scalability lost via ghost-hydrogens. Thanks to Paul Rowland for assistance in discovering this issue. * fix extraction of previous X-ray weight from input PDB file: if recorded several times in REMARK 3 section, the first value is taken. Also: fix reporting if recorded X-ray weight is outside some very generous limits. * during water-update: an error was triggered (wrongly) if initially added waters were completely removed in a subsequent stage - added check for this. * slight change in logic for excluding duplicate restraints (to avoid having same restraints in both the residue dictionary as well as the linkage dictionary). This should get rid of a few failures with 'something wrong when excluding XYZ restraint from ...' messages. * pickup any TLS-parameters after doing a rigid-body cycle. Thanks to Direk Kostrewa for reporting this issues. * pdbchk: * work around "egrep: Regular expression too big" error on OS X Lion (10.7) * Fix "grep: repetition-operator operand invalid" error on OS X Mountain Lion ##### Grade: Improvements: * Grade now provided on the Grade Web Server http://grade.globalphasing.org This is useful for users without a CSD system licence working on non-confidential ligands. * Introduce override values for geometry around phosphates where mogul does not have an opinion, since RM1 does not handle phosphates well. The biggest improvement is for polyphosphates found in cofactors like FAD, ATP and NAD. * "Planarity vetoes" from Grade. Mogul information is now better used to ensure that torsions like the central one in biphenyl are not wrongly set planar when CSD distribution clearly shows a range of values. * set atomnames if supplied with mol2 with all atoms being named after their element type ("C", "N" etc). * Mogul search performed by Grade modified to allow small amount of generalisation for bonds and angles but not torsion angles. This allows better use of information from highly related CSD structures. * Introduce option -really_noH for ligands that do not have any hydrogen atoms. * grade_PDB_ligand has been switched to use v3 atomnames. * grade_PDB_ligand option -xdat to use experimental coordinates from LigandExpo when no ideal coordinates are available. * grade_PDB_ligand option -nonet to allow use from behind firewalls that prevent the tool getting direct web access. * recognise-compound utility added to find whether ligand is already in PDB chemical components definitions. This is run by Grade on every run to provide a warning that a user's new compound is already a known PDB chemical component. * Support for CSDS 2014 release of Mogul. Detect and cleanly exit if mogul stalls on initial dependency check. This should enable quick diagnosis if mogul stall problem with NFSv3-mounted CSDS occurs. See http://www.globalphasing.com/buster/wiki/index.cgi?SoftwareMogulRelease2014NFSissues * Improve information about methods used in output CIF to include Mogul version, CSD version, use of additional corporate data and actual QM method used (for example RM1). * introduction of -shelx option to output restraints file for SHELXL. Thanks to Julian Holstein for help in developing and testing this new feature. * clean up unhelpful REMARK records in output pdb. Fixes: * Fix issue with torsions not being enforced during QM step of Grade * Grade bug failing to clean up temporary directory on exit. * protection against Mogul run away process with malformed mol2 files. * mol2 files containing positively charged phosphorous atoms will now work. * mol2 files with titles with comments containing string "_ideal.pdb" will now work. ##### Dictionaries: * Dictionaries for iron sulfur clusters FES and SF4 added. These were produced manually using CSD information. * Dictionary for vitamin B12 (cobalamin) added. This work showed up serious issues in CCP4 and PDB definitions for B12 see http://www.globalphasing.com/buster/wiki/index.cgi?B12Dictionary * Improve contact distances for Be and Fe atoms based on CSD information. #### EditREFMAC changes: * Improve EditREFMAC's handling of quoted data - Quoted data values in the input refinement dictionary are now handled correctly - Data values that contain spaces or single quote (') characters are double-quoted when saved (even when not strictly required by the CIF format) - Input refinement dictionaries containing double-quotes that are not used for quoting data values are rejected by EditREFMAC (for example an atom name like HO3") - If the user has edited any data in EditREFMAC so that they contain double-quote (") characters, the user is warned when the edited data are saved that the result may not be usable. * Fix misfeature that could cause loss of user edits - If user clicks "Save Table" while actively editing the contents of a cell, the edited contents of the cell are now saved rather than the unedited contents. ################################################################### # # Below are the release notes of the previous BUSTER version 2.10.0 # stable (released 20 July 2011). # ################################################################### BUSTER 2.10.0, the production release of July 20 2011 incorporates the cumulative changes listed below for the beta releases of 20 Jul 2011, 17 Feb 2011, 11 Nov 2010, 8 Oct 2010, 30 Apr 2010, 26 Mar 2010 and 05 Nov 2009. ============================ Beta release of Jul 20 2011 ============================ ##### BUSTER and autoBUSTER toolbox: Changes: * autoBUSTER (refine command) will not use Hendrickson-Lattman coefficients by default. To enable the use of Hendrickson-Lattman coefficients during refinement, the column labels need to be specified as part of the command line with eg. autoBUSTER_hls="HLA,HLB,HLC,HLD". * We now default to using MakeLINK (instead of pdb2seq) to generate TNT sequence files. This should especially deal better with LINK cards from the supplied PDB file as well as using better restraints for glycosylation. * The automatic generation of dictionaries based on current coordinates (as a last resort) has been disabled. The user is required to provide a restraint dictionary for novel ligands. * We now supply Grade CIF-format dictionaries for the most common cofactors, buffers and cryoprotectants in $BDG_home/tnt/data/common-compounds. These have all been checked to produce sensible results for existing PDB entries. The old dictionaries that were distributed in $BDG_home/tnt/msd and $BDG_home/tnt/ccp4 have been removed. * A detailed discussion covering recent changes in restraint dictionary tools and handling is available on the BUSTER wiki at http://www.globalphasing.com/buster/wiki/index.cgi?BusterLigandRestraints More details can be found at http://www.globalphasing.com/buster/wiki/ Improvements: * An added check within the 'pdbchk' tool will be performed: to deal with renamed RNA residues (Ar, Cr, Gr and Ur instead of A, C, G and U), e.g. coming from Coot. * refine: robustify checking of CRYST1 record * corr: work around some limitations in overlapmap * pdbchk_element: update to components.cif as of 20110702 * The BUSTER_TLS_SET usage has been improved: - automatically fuse multiple sets specified by curlys - detect and warn if there are multiple tokens on record * The various command-line programs from the autoBUSTER toolbox will now report the date of the release (and not the date of the last change to that particular command/module). This will make support requests much easier. * We now save a copy of all user-supplied and automatically fetched CIF dictionaries in subdirectory restraint_dictionaries Fixes: * pdbchk: - Fixed length of comparison with residue name (in pdbchk_element) - Fixed problem when removing lines left by MOLREP program - Fixes related to ordering of records following PDB standard - Protect StandardRecordOrder from hiccup with user specified pattern containing underscores * pdbcmb: keep top-remarks added by autoBUSTER * consolidate treatment of non-standard initial REMARK records with new parameter: RemoveOldNonStandardInitialRemarkSection default is "yes" * pdb2tls: - also print serial number in REFMAC mode - detect sequence specification without a chain name in the second token * add protection against dash failing on 'empty' .autoBUSTER files * fixup extracting TLS info from LIST.html when not doing Gelly refinement eg. in MapOnly mode * write long space group name to MTZ file header * fix some grid sampling restrictions (A2, I2, I21, I4/m) * pkmaps and frcdis: robustify licence checking * pkmaps: - robustify treatment of erroneous input - fix spurious pkmaps crashes of the type: "unable to map point into map" Thanks to Xavier Robert for providing a test case. * mol2_to_cif: - Better handling of lower-case letters in atom names (Cl, Br) - Better handling of triple bonds - Use ASUNK for unknown arsenic - Handle six-column mol2 files without segfault * MakeLINK: - Fixup sorting residues with negative numbers - Correctly handle disulphide-bridges for vicinal CYS residues - Fix handling of GXPEPTIDE links given as LINK cards * TNT: up various static array sizes to deal with larger models and more reflections * install scripts: further robustification ##### Grade * Write report on restraint sources into the output CIF file * Report the version of mogul used * improve handling of mol2 files. In particular mol2 files without charges are now correctly parsed. #### NOTES The 32-bit Linux distributions of Global Phasing's software will work on systems running relatively old kernels (versions 2.4.x). Most mainstream server and desktop Linux distributions that are currently under active maintenance are based on the newer 2.6.x kernel series. The current 32-bit release will be the last to support Linux systems based on the 2.4.x kernel. Future distributions (including patches and minor updates) of our software for all Linux systems released after this one can only be relied on to work on systems running kernels from the 2.6.x series. This is only a significant change for our 32-bit distribution: our 64-bit distributions for Linux have always required kernel version 2.6.x To check the version of the kernel on a particular system, run the following command: uname -r ============================= Beta release of 17 Feb 2011 ============================= * BUSTER reference card. This is a two page document that lists the most useful options for refine and grade. It is supplied as a pdf document to be printed double sided on to a card. ##### Grade: New features: * In response to a user request, added the -bigplanes option so that the output dictionary contains large planes rather than the default where four-atom planes are produced. This option will make the planarity significantly more tightly restrained. Improvements: * mol2 coordinate files now handled by Grade using its own code, rather than libcheck as previous releases. This enables better atom typing particularly avoiding problems with thiophene-type sulphur atoms. We recommend using mol2 format, with all hydrogen atoms present, or SMILES input when using Grade. * torsion restraints produced by Grade improved. Uses mogul information to set 3-fold staggered torsions for bonds joining two sp3 type atoms. Previously these could be fixed at a single 180 degree torsion, or be left free to rotate. * Documentation moved to the BUSTER wiki in anticipation of imminent release to general academic users. The BUSTER wiki is not password protected so documentation should be easier to find. Fixes: * can now handle the (syntactically-incorrect) CIF restraint dictionary files produced by Corina on structures without chiral centres * In response to a user request, Grade now outputs ideal-coordinate PDB file with an occupancy of 1.0 rather than zero. ##### Gelly: Fixes: * bug fixed in and new features associated with -qm option (see below) ##### BUSTER and autoBUSTER toolbox: New features: * new ShortRun macros for running a short refinement after some rebuilding (eg in coot) of a previously BUSTER-refined structure. Use 'refine -M list' for a full description including a link to a page on the BUSTER wiki describing how and when the macros should be used. * the eh99_protgeo.dat protein dictionary now includes hydrogen atoms. Restraints for hydrogen atoms have been checked to yield sensible geometry. * A new tool is available: 'hydrogenate'. This allows the addition of hydrogen atoms to proteins and/or ligands. It uses the 'reduce' tool from molprobity but extends this to ligands described by REFMAC/CCP4-style CIF restraint dictionaries, such as those produced by Grade. 'hydrogenate' is particularly useful for refining proteins at resolutions better than 2.0 Angstroms and for the -qm option. * fix for hydrogen atoms and zero-occupancy atoms: they are now both excluded from the bulk-solvent masking (whereas before they were only excluded if void correction or one of -L, -Lpdb or -x was used). There are indications that for fully hydrogenated proteins the maximum likehood X-ray calculation could be improved, this will be included in a future release. * added parameter AutomaticFormfactorCorrection (default=no) to adjust formfactor for each element in input PDB file automatically * new utility 'graph_autobuster_recipCC' to facilitate looking at the reciprocal-space correlation coefficient plot that BUSTER produces. This plot can reveal problems in the data collection/processing stage, such as: low resolution overloads, data anisotropy and ice ring contamination. It can also reveal inadequacies in the weighting of phase information from partial MR models in certain situations of severe incompleteness. Gerard recommends that the reciprocal-space correlation coefficient plot is routinely examined and the new utility makes this easier. More details on the BUSTER wiki. Improvements: * BUSTER wiki now includes more details, examples and discussion. * the distributed samples/autobuster directory now has a single quick to run example. * -l added better detection for the input dictionary is CIF or TNT or some other format (e.g. containing Gelly commands). You are recommended to directly use refmac-compatible CIF dictionaries (from Grade or 3rd party tools) and not convert them to TNT format. * gelly_refine: added -Gelly command-line option and use the same logic as in 'refine' for the '-l' flag. * -qm option to use the weighted quantum chemical energy of a ligand as a restraint function in refining protein ligand complexes: * An initial check is now made to ensure that hydrogen atoms have been added to the ligand before QM can start. The 'hydrogenate' tool (see above) makes it easy to add hydrogen atoms to a ligand. * A GAMESS helper perl script now available to allow the use of ab initio and DFT methods using the GAMESS package, available from the Gordon research group: http://www.msg.chem.iastate.edu/gamess/ The helper can be downloaded from the BUSTER wiki and could be adapted to allow use of other quantum chemistry programs. * Use of -qm in refinement now summarized in a output pdb file REMARK. * Documentation of -qm much improved and moved to the BUSTER wiki in anticipation of imminent release of -qm option to general academic users. The BUSTER wiki is not password protected so documentation should be easier to find. Fixes: * dealing with user-supplied macros better by handling - superfluous spaces around the '=' character - CRLF line terminators * corrected problem in ana_pdbmaps that could affect resulting clusters (in finding padded PDB limits in fractional coordinates) * fix regression in pdb2cor where residues in inter-chain linkages were written at the top of the output PDB file * robustified the licence checking mechanism * improved the command line checking wrt. arguments being numbers * on request from PDBe have removed units from the REMARK 3 lines on the T, L and S tensor cards. Likewise removed the ALL ATOMS and OTHER ATOMS entries * corr: better handling of chains with negative residue numbers * mtzchk: robustify the handling of odd space group symbols * pdb2seq: further improved automatic detection of inter-chain SSBONDS * pdbchk_element: always automatically correct element type of hydrogen atoms in THR, VAL, ILE and GLN residues when borked by external programs * pdbcmb: improved the automatic ordering of records * pkmaps: fix some infrequently used interpolation options * BUSTER: deprecate use of old scaling, old optimiser and old structure factor engine/convolute mechanism * BUFFET: made obsolete by autoBUSTER toolbox. Please do let us know of any features which are not covered by autoBUSTER ============================= Beta release of 11 Nov 2010 ============================= ##### Grade: Fixes: * fix to link library bug that prevented Grade running on OSX * add missing package declaration (bug affected some CentOS and RedHat systems) * mogul search performed by Grade now has generalisation turned off. Generalisation in mogul widens the search if few hits are found and can mean that non-relevant data is considered and erroneous planes produced. * Grade dictionaries should now be correctly interpreted by refmac (names for planes now shortened to less than 8 characters). * correction to final REMARK 3 information in autoBUSTER pdb file if a Grade dictionary is used ##### Gelly: None. ##### BUSTER: None. ##### autoBUSTER toolbox: Fixes: * pdb2cor: added work-around to deal with incorrectly placed TER records * added several work-arounds to deal with MMDB issues (through CCP4 programs like PDBSET). * better handling of cases where some (but not all) non-standard residues are given by a user-supplied dictionary ##### Dictionaries: None. ============================ Beta release of 8 Oct 2010 ============================ ##### Grade: * Initial release of this new ligand-generation tool. It uses statistical information from the Cambridge Structural Database, along with semi-empirical quantum methods, to generate good restraint dictionaries from a variety of input formats. ##### Gelly: * Support for the use of quantum chemical functions as restraint functions for ligands for use in refinement with autoBUSTER and in QM geometry optimization with gelly_refine. ##### BUSTER: New features: * BUSTER (through autoBUSTER) can now directly use the weighted quantum chemical energy of a ligand as a restraint function in refining protein ligand complexes. By default the method uses semi-empirical QM methods such as RM1 with helper executable using the fdynamo program library developed by Prof. Martin Field and co-workers (http://www.pdynamo.org/). The fdynamo helper is supplied with BUSTER. Use 'refine -h' to see the options which are used, this leads you to a wiki page describing how this technique can be applied. Fixes: * several small modifications to enable use of latest Perl 5.X versions (e.g. 5.12) ##### autoBUSTER toolbox: Improvements: * when we need to create a new set of test-set flags (FreeR_flag), allow the user to override default parameters: Mtztools_FreeRflag_FrcMin=0.05, Mtztools_FreeRflag_FrcMax=0.10 and Mtztools_FreeRflag_NumAim=1000 * new parameter BusterFreeFlagValue (default=0) to explicitly set the FREFLG value for BUSTER * added check to catch inconsistent spacegroup name/number (mostly if the number doesn't follow the CCP4 N+{1000,2000,3000,etc} system * make the non-standard top header in the final refine.pdb customisable with parameters NonStandardInitialRemarkSectionCard=REMARK and NonStandardInitialRemarkSectionDelimiter=yes * also write resolution range after reporintg final/best R and Rfree on standard output. * pdb2seq: more robust handling of SSBOND cards - take symmetry information into account to decide if we should have SS linkages on CHAIN or RESIDUE cards * allow several dictionaries to contain the same residue name when testing for atom name mismatch: only if the last one also shows mismatch will we try and generate a new entry via PDB2TNT - otherwise we take the first dictionary that showed no mismatches * pdbchk: several new checks * PdbChk_SsbondHasRecordAsStars (deal with SSBOND records containing '*' characters in record number - from molprobity/reduce at least) * PdbChk_DnaResiduesFromCoot (deal with Coot's feature of renaming DNA residues to Ad, Cd, Gd and Td instead of A, C, G and T) * check that atom names don't contain comma characters * check (and fix) if PDB file has DOS-style CRLF line terminations * new parameters MissingAtomsBfac, MissingAtomsBfacSigma (and MissingAtomsBfacFactor=1.25 plus MissingAtomsBfacSigmaFactor=0.125): defaults to Wilson B (times Factor) or (if Wilson B can't be determined) to 150.0/15.0 * added option (SequenceFileGeneration, default=pdb2seq) to use MakeLINK for generation of TNT.seq file * added new parameter ReuseGeometryFile=yes to reuse the restraints from first big cycle in subsequent cycles. * pdbchk_element: update to components.cif as of 20100820. * supersede TLSInitialiseBiso with general InitialiseBiso parameter Fixes: * refmacdict2tnt: conversion of CIF chirality records with volume sign 'negative' is now correct * better handling of allowed test-set column names in pattern matching * handle parameters where the value contains multiple spaces correctly on the command-line * Pdbset(mmdb) does not deal correctly with eg. atomic charges like: O1-. There are also other issues with pdbset, so avoid using it eg. when setting the space group in a PDB file. * added check and warning if macro filenames contain characters that will confuse the sh-syntax later on * Fixup sorting water chains to the top. * Several fixes when dealing with restraint dictionaries: we have standard dictionaries, our own supplied dictionaries, a user-supplied dictionary in various formats and sometimes we need to generate restraints on-the-fly. All this needs to be done in the correct order and with all the appropriate checks (to see if a given residue name in the PDB file means the same thing in the dictionary file etc). * fix ordering of records in final PDB file when some came initially after CRYST1 ##### Dictionaries: Fixes: * Some contact distances have been fixed - various new structures involving nucleic acids and heavy alkaline-earth metals indicated that distances like Sr-N were too pessimistic ##### MakeLINK: Improvements: * MakeLINK inserts bonds based on the elements at either end of the LINK, rather than on input geometry, for LINK cards not corresponding to well-known linkage geometries * LYS-PLP, CYS-BME, HIS-FAD geometries recognised automatically when LINK cards are present * MakeLINK handles nucleic acid chains better Fixes: * MakeLINK no longer ignores LINK records between atoms which are not in close contact. ============================= Beta release of 26 Mar 2010 ============================= ##### Gelly: Improvements and changes: * Correct handling of ideal distance contacts for hydrogen atoms involved in a hydrogen bond. Fixes: * Produce useful information when bond setup causes problems because of duplicate bond angles, in replacement of the previous message "impossible(?) error in storing angles". * Target restraints setup: improve error message for duplicate atoms in target structure. ##### BUSTER: Improvements and changes: * Add formfactor for N+1. * Allow up to 512 SSBOND records (TNT). ##### autoBUSTER toolbox: New features: * Support for refinement of ligands with hydrogen atoms. The solvent mask calculations will still ignore hydrogen atoms to avoid bias. * Additional choice of water-update routine (-M WaterUpdatePkmaps): this uses the same default program for analysing difference density peaks and existing waters, but new waters will only be placed close to existing hydrogen partners (in the macromolecule). Improvements and changes: * Much improved conversion of refmac-compatible CIF-format restraint dictionary by new tool refmacdict2tnt. In particular ideal distance atomtype is converted. This tool is used on any CIF-format restraint dictionary supplied to autoBUSTER by a '-l' argument. * Online help ('refine -h') has been improved to give available arguments in order of importance (and logical groupings). * pdb2tls: default automatic definition is now identical to the '-M TLSbasic' macro (i.e. EachMacroMolChain). * pdb2tls: improved handling of phenix.refine PDB files. * A new parameter (IncludeNonStandardInitialRemarkSectionInFinalPdb with default = yes) is provided to switch off addition of the top (non-standard) REMARK section in final output PDB file. * The defaults for KeepZeroOcc and KeepHydrogens has been changed from 'no' to 'yes'. So all hydrogen atoms, as well as atoms with an occupancy of zero, will be kept throughout the refinement. However, both types of atoms are excluded from the bulk solvent masking. This means that ligands can be refined with zero occupancy hydrogen atoms included. * The 'pdbchk' tool now also checks (and fixes) PDB files coming from the MOLREP program: those files often contain lines starting with '#' to denote separate domains or molecules. * 'pdbchk' also checks/fixes a missing newline at end of PDB file. * Macros now allow setting parameters explicitly before the last cycle (even if the exact number of BIG cycles isn't known beforehand). * pdb2occ: handle insertion code when writing the Gelly commands. * Significant improvements in documentation, with updated list of parameters and more detailed sections dealing with rigid-body refinement, TLS, NCS, ligand-chasing (-L/-Lpdb) etc. * Robustified handling of command line arguments by type checking. Fixes: * When pdb2tls is used to automatically define TLS groups, but the molecule(s) are smaller than the current default (i.e. less than 100 atoms): give warning and switch off TLS usage. * When removing files from different UNIX groups, the 'refine' command might have hung: this has been fixed. * Running a subsequent 'refine' job inside a previous output directory should now be possible. * Fixed typo when getting sc-CC in single-chain models. ##### Dictionaries: * added carefully checked restraints for heme type HEC to cofactor_geo.dat. * TNT bad contacts now include hydrogen atoms. * Ideal distance contact library now has default UNK terms for hydrogen atoms and halogens. * Fixed chiral term for HYP. * Fixed some incorrect angles for d5'PEND and 5'PEND in nuclgeo.dat. ============================= Beta release for 5 Nov 2009 ============================= ##### Gelly: new features: * Gelly now ignores pseudo-chiral centres. These are CHIRAL restraints where two atoms involved are equivalent. This often happened on sulfates and phosphates and could result in very ugly "umbrella" conformations. improvements and changes: * Better handling when supplied with two atoms that are exactly on top of each nother. This now produces a sanity failure rather than a numerical error. If wanted Gelly can push the two atoms apart. * Option to use protein dictionary with peptide omega restrained by a torsion angle term rather than a plane (protgeo_eh99_omega_torsion.dat) ##### BUSTER: new features: * Support for some non-standard space group settings - A2, C21, I2, I21, P2122, P2212, P22121 (not yet P21221) Requires a specially patched version of sftools, for which you are referred to the Phase IV Wiki: SoftwareReleases -> known issues (descriptions and fixes/patches) -> PatchingSftools improvements and changes: * Support for 64-bit versions of all programs on Linux * Reduce the amount of memory needed for buffers in masking step by 25% in the usual cases ie. when not using the 'missing-atoms' channel * During ncsmask step detect if folding back to unit cell is required and automatically do the folding * Establish the server-client socket in BUSTER_socketdir (defaults to '/tmp') * Support for up to two million reflections (TNT) ##### autoBUSTER toolbox: improvements and changes: * make it possible to switch off the use of Hendrickson-Lattmann coefficients (HLs) by setting autoBUSTER_hls="no" * added check to stop on different spacegroup in MTZ/PDB file * improved check for a working CCP4 installation (as part of 'mtzchk') * the supplied example script for using Coot's 'findwaters' tool has been improved: added more checks for finding the findwaters binary and a patch to deal with Coot renaming residues (e.g. RNA/DNA) * added check that Rfree doesn't go above 1.0: exit with error message in those cases * plotmtv should be on users PATH after installation (this program is used to visualise graphical results in *.mtv files) * enable setting the mean electron density of both macro-molecule and solvent: RhoMacroMol and RhoSolvent, respectively * updated syminfo.lib and symop in $BDG_home/database to the versions slated for CCP4-6.1.3. This includes the renumbering of 3004 to 5005 fixes: * fixed problem when dash is the default system shell (i.e. called when running /bin/sh): 'pdb2tls' was misbehaving under those circumstances. * fixed a bug in 'pdb2occ'that could have resulted in not all required BUSTER_COMBINE cards being written, i.e. getting different occupancies for atoms that belong to the same alternate conformation (reported by a consortium member). * set GeometryWeight_ideal=0.0 when doing rigid-body refinement (should have been already in the previous release but got overlooked) * fixed a typo that caused completeness to be calculated incorrectly and put into REMARK 3 section of final PDB file. * fixed logic in finding syminfo.lib as part of the 'pdb2dpi' tool * translate spacegroups of form "P1212" etc into "P21" etc * several fixes for detecting, handling and deducing element information in PDB files (as part of 'pdbchk' section) * fixing sorting of output PDB file to follow closer to given sequence order (chain linkages confused this) * pdb2tls has seen a variety of fixes and improvements (after analysing all PDB entries with TLS information) * fixed sequence issue when adding TLS-contributions in presence of inter-chain SS-bonds. Effect is that chains are now sorted according to the TNT-sequence file * ensure input files are handled correctly (if they e.g. contain a relative path) * make it unnecessary to specify UseNmissLastCycle=yes after having set UseNmissThroughout=yes * make it unnecessary to specify UseMaxEntLastCycle=yes after having set UseMaxEntThroughout=yes ##### Dictionaries: * improved chirality information used for common cofactors =================================================================== Beta release of 22 Jul 2009, on which the production release of July 2009 (version 1.6.0) was based =================================================================== ##### Gelly: * -autoncs now has an automated weighting scheme that takes into account the number of chains in an NCS group. ##### BUSTER: * Fix resetting of bounds for B-factors: This allows TLS refinement to run to completion much more often. * Fix the internal scaling used for the rigid-body part of TLS. * Fix a corner case in the scaling module (ALABASTER) when the data are far from absolute scale. ##### autoBUSTER toolbox: * the QuickMap macro has been renamed to MapOnly * Make gelly_refine run on Darwin. * Fix a corner case in pdbtools to prevent an infinite loop when removing atoms with zero occupancy. * pdb2occ: fix when alternate conformations are for single-atom residues (like waters or metals) * give a bit more information for the (default) final void analysis step * added check that given X-ray weight is in allowed range * added checks so that -RB/-TLS flags (which have optional arguments) don't get confused by immediately following par=value settings * give warning if a fresh test-set needs creating ============================ Beta release of 8 Jul 2009 ============================ ##### Gelly: new features: * Much improved geometry function for BUSTER refinements. In particular, non-bonded contacts are more realistically modeled using an ideal-distance contact term in place of the previously used TNT bad contacts. The ideal-distance contact term is also used for 1-4 interactions resulting in improved Ramachandran statistics. Protein Bond and bond angle terms now use the Engh & Huber EH99 restraints in place of the earlier EH (1991) values (see dictionary section). * Refinement with the improved geometry function generally results in slightly lowered Rfree, improved Rfree-Rwork gaps and much improved Molprobity scores. The use of the ideal distance contact term will also lead to more realistic restraints on short protein-ligand contacts and the prevention of eclipsed torsions within ligands. * Support for TLS (see BUSTER section). improvements and changes: * Better treatment for atoms and ions on special positions. In particular sulfate ions at special positions are automatically recognized. * Much improved information in PDB REMARK 3 section. This includes adding descriptions of what is in each dictionary used, the use of -autoncs and -target LSSR options. fixes: * TNT atom selections involving ranges such as {A|1 - A|957} are now done numerically so that gaps in the sequence will not cause an error. * Early recognition of numerical problems (NaN values) in gradient calculation. ##### BUSTER: new features: * Support for TLS refinement of an unlimited number of groups. - Generally, we have found that the use of a single TLS group per chain often gives much of the benefit that can be obtained from a complicated decomposition. However, of course, in some complexes where chains are strongly entangled, the natural TLS domains will need customised definitions. - The low-level machinery to compute structure factors and gradient components by Agarwal convolution when anisotropic B-factors (actually, anisotropic U's) are specified has been implemented in TNT including the use of openMP capabilities. The input/output and optimisation mechanisms for TLS are implemented in Gelly. - An easy method to get TLS refinement going is to use the macro TLSbasic * Compute overall CC(Fo,Fc) for work, free and total. At each iteration this is written to: shell.01/reciprocal_CC.txt. * Collect overall values of the Log Likelihood for total, work and free reflections at each interation. This is written to: shell.01/mxl.txt. * Support for running on Darwin (Intel). * Support for computing structure factors and gradients when some atoms are anisotropic. * Support for more atoms (up to 200 000) improvements and changes: * Release memory for maps before entering Gelly. * Set range of CC-plots to just below zero and just above one for easy comparison. * New binning routine. * Increase range for a free flag from [0-49] to [0-99]. * Allow for setting ranges for scaling parameters (see -CS command-line flag for 'refine' command) * Update to newer PETSC (2.3.2.p10) and TAO (1.8.2) libraries. * Link against CCP4 version 6.1.1 (patched). fixes: * Compute R-values on observational scale. * Fixup finding the TNT symmetry information file, e.g. for "P 1 21 1" when running through Buffet. * Fixup generation of R_Rfree.html if there are empty bins. * Remove support for PlotIt13 ##### Dictionaries: new features: * Engh & Huber (1999) restraints are used for proteins; in particular, cis- and trans-proline are now distinguished. * Torsion restraints for proteins have been very carefully checked and are now active by default. Proteins and nucleic acids have atom-typing which, in conjunction with the new ideal-distance contact term, provides a 1-4 term making many implausible conformations strongly disfavoured in optimisation. * The dictionary format now allows the inclusion of ideal-distance contact information via atom typing, and this information has been included for proteins, nucleic acids and commonly-found ligands. improvements and changes: * Sugars now have enforced chirality agreeing with the PDB; there are optional chiral linkages to enforce biologically-correct chirality of glycosylation. * Some common buffer molecules have curated geometry restraints and atom typing; we now agree with the PDB as regards the names and geometries of the many variants of DTT. fixes: * Corrected some missing angle restraints on nucleic acids and protein termini * Leaving-atoms added to sugar descriptions, so restraints are now correct for both polysaccharides and isolated sugars * Improved descriptions of chiralities of cofactors * Azide is now restrained as linear rather than bent, and some quaternary ammonium geometries made more plausible. * Introduced new BCORREL terms for haem based on unrestrained re-refinement of very high resolution structures * MakeLINK now handles RNA more correctly, recognising some more of the common modified bases. ##### autoBUSTER toolbox: new features: * New tool visualise-geometry-coot for allowing users to run efficiently through lists of geometry problems in the context of the structure and electron density; this is a very useful counterpart to the list of difference-density peaks already available from coot. * pdbchk will check (and optionally fix) the position of an OXT atom within a residue: for the internal conversion routine this needs to be at the end of the residue * warning messages from Gelly (during initial sanity check) are now presented in main logfile (i.e. stdout) * command-line flag (-w ) for easier setting of initial X-ray weight * user can explicitly specify a set of Hendrickson-Lattmann coefficients using the autoBUSTER_hls parameter * command-line flag -nthreads (to specify number of CPUs/cores to use) * macro feature: see 'refine -M list' for a list of pre-defined macros and documentaiton about concept and user-defined macros * support for TLS refinement (-TLS flag) * tool to extract TLS information from PDB file header or to generate simple TLS parametrisation: pdb2tls * tool to generate template for occupancy refinement (alternate conformations, partially occupied residues etc): pdb2occ * tool to calculate DPI values: pdb2dpi. THese are now generated by default and placed into REMARK 3 section of final PDB file * New tool pdbvconv (now used automatically in pdbchk) for converting PDBv3 input to the PDBv2 format used internally; includes an automatically-generated complete list of atom names that changed between v2 and v3. * sourcing the $BDG_home/setup.sh or $BDG_home/setup.csh scripts (for setting up the proper environement for running BUSTER) now removes all references to older installations before setting up a clean environment. This will make it easier in the future to switch between different versions of the program. improvements and changes: * final results file (refine.mtz and refine.pdb) are now both files instead of symbolic links * report number of swapped and/or pruned residues (if RunBusterPrintUsefulInfo is set to yes): mostly of interest for refinements with LSSR_type NCS restraints. * X-ray weight now reported (and used) in correct units (instead of x100 as before) * added some safety net when running with missing atom channel active * changed B-refinement scheme defaults so that we basically only ever decide between 'individual' and 'None' * allow several column names for test-set flag - currently FreeR_flag and FREE (but expandable) * new/changed defaults: - 100 small cycles - UpdateWaters=no (i.e. -noWAT); to switch it on use -WAT flag. - low-resolution cutoff now less sudden: only kick in after big cycle 2 and restrict lowest resolution bin only partly. - BUSTER uses an improved (resolution) binning mechanism: this can give different results, but avoids using too many bins with very few reflections or a ridiculously small amount of bins for large numbers of reflections (previously this was basically fixed at a value of 9 bins). * pdbchk will now check for PDB v3 versus v2: internally autoBUSTER currently uses v2 (and final output PDB file will also be v2) * old flags -n/-N now called -nbig/-nsmall * exact command-line now printed with line-break (and \-character) at top of refine.pdb * if input PDB file contains the recorded X-ray weight, this will be used as a starting value (parameter StartFromPreviousWeightInPdb) * print anisotropic B-factor scales and Luzzati error to meaningful precision in REMARK 3 section of refine.pdb * implemented an option (CorrRunSeparateChains) to calculate CC values separately per chain instead of all chains in one go: this is required for large structures with lots of chains (since otherwise the ATMMAP runs out of integers) * possibility to use fixed solvent scales (might be necessary for very poor models or very low resolution date): FixedSolventScales parameter * added test PdbChk_IleResidueWithAtomCd to deal with PDB files coming out of phenix.refine (or CNS/X-PLOR) * added test to check CCP4 right at the start: MtzChk_WorkingCcp4 * added parameter (KeepFromEnv_ccp4) to enforce using CCP4 from current environment fixes: * resolution limits from different sources (user or MTZ file) are now synchronised so that values in REMARK 3 section of final PDB file should be correct. * fixed UseGapAsBreakInSeq feature in pdb2seq * keeping hydrogens (e.g. on ligand) now works correctly with PDB2TNT (generating dictionary frmo existing structure) * Fixup sorting with negative residue numbers in pdb2seq * renamed pdb2tnt to ab_pdb2tnt to avoid clashes with PDB2TNT on case-insensitive HFS+ filesystems * Take HETATM records into account due to MSE residues: this should support Se-MET structures better * fixed detection of system-wide .autoBUSTER file ============================= Beta release of 11 Jul 2008 ============================= ##### Gelly: new features: * NCS restraints - The use of Local Structure Similarity Restraints (LSSR) is a major new development in this release. The concept of LSSR is novel: it is not based on the 3D superposition of coordinates, but instead works by restraining corresponding local interatomic distances to be similar. A plateauing functional form is used for the restraint. LSSR are much easier to use than the conventional "soft" NCS restraints. In particular, the need to prune out regions of the structure that violate NCS is markedly reduced. In addition, because of the local nature of LSSR, domain-type motions are allowed to take place without any manual intervention. The autoBUSTER command line option -autoncs automatically identifies NCS relations and sets up the corresponding LSSR restraints. * Target restraints - LSSR can also be used to exploit pre-existing knowledge that the structure under refinement is similar to another already solved structure, called the "target". The target structure remains fixed during refinement. For instance a high-resolution apo structure can be used as a target when refining a lower-resolution ligand-soaked molecular replacement structure. Use of LSSR in this case produces improved Rfree together with better geometry validation scores. The method is also particularly applicable to the refinement of proteins with multiple crystal forms. The autoBUSTER command line option -target facilitates the easy application of target LSSR. * Procedure for swapping equivalent atoms to improve NCS and/or target restraints. * Utility restraints on the angle between any three given atoms. An example application of this is to allow the definition of restraints on the geometry of metal binding sites, such as tetrahedral zinc sites. * Utility restraints on the torsion angle between any four given atoms. The restraint function takes the form of a sinusoidal penalty. A potential application would be to ensure that an aliphatic part of a ligand is encouraged to remain staggered. improvements: * More helpfully worded messages upon failure of sanity checks. ##### BUSTER: new features: * use FFTW for P1 transforms (solvent, prior and MaxEnt) New keyword: FFTW={0,1} to dis-/en-able. Default is enabled. improvements: * improved handling of 'unknown' element type 'X '. fixes: * [cmdServer]: fixup a signal race. ##### autoBUSTER toolbox: new features: * give short summary about severe outliers before and after each BIG cycle * better automatic assignment of atom type to PDB records to use correct form factors for each atom. Columns 77-78 on output PDB file should show correct atom type. improvements and changes * can now specify which checks on PDB files should not be done in "pdbchk" (parameter PdbChk_ChecksNotToDo) * the automatic restiction of poor low-resolution can now be controlled using parameters AutomaticRestrictLowres, AutomaticRestrictLowresCcCut, AutomaticRestrictLowresBinCut, AutomaticRestrictLowresFromCycle. The current defaults make autoBUSTER behave as before. * the command-line flags -Edat, -f, -t and -Ncs are now deprecated (but still recognised). Using -Gelly instead should give the same results. * additional command-line flags added that are passed directly to Gelly: -autoncs, -target:f, -autoncs_weight, -target_weight, -sim_swap_equiv, -sim_swap_equiv_plus, -glim, -screen:i, -screen_sigma, -autoncs_noprune, -dlim, -keeppdb See Gelly documentation for details. * several -Gelly cards can now be given on the command-line. * show real-space CC plots always in range 0.0 - 1.0 * output basic REMARK 3 information about NCS and TARGET restraints * the values for selecting the 'interesting region' (during ligand detection with the -L and -Lpdb argument) are now under parameter control: AnaPdbmapsMinVol, AnaPdbmapsPadding, AnaPdbmapsCut1, AnaPdbmapsCut2 * detection of 'interesting regions' now much faster * new flag -noNORM to prep_FitMAP (to supress normalisation of maps). * update to handle PDBv3 components * check that PDB files and MTZ file are of this type (in case of giving the wrong file name for a specific flag) fixes: * updated link to current PDB format * the logic for the formfactor correction was wrong (taking CuKa values as a base-line): this has been corrected. * better dealing with atom or residue names that contain '*' character * when checking special linkage descriptions in a (user-supplied) TNT sequence file: deal with continuation lines and linkages specified on CHAIN record (i.e. inter-chain linkages). * make sure final MTZ file is in standard CCP4 asymmetric unit * generation of cluster.lis by prep_FitMAP had problems when encountering more than 10 regions. * all scripts: improved handling of UN*X utilities: head, tail, sort, echo on different distributions and platforms. ============================= Beta release of 15 Feb 2007 ============================= new tools/programs: - pdbchk: new program for extensive checking of a PDB file. In 'fixing mode' (i.e. if an optional output file name is given) it tries to correct some of the more trivial problems it encounters. The checks are for conformance to the PDB format specification (up to a point), but also for some autoBUSTER-specific requirements (like missing chain identifiers). The goal is to ensure maximum compatibility of the PDB file with the autoBUSTER refinement toolchain. - pdbcmb: will combine two PDB files (old and new) to produce an output PDB file that will contain everything from new PDB file plus any PDB header records only present in old PDB file. This is mostly used internally to carry through all header records of input PDB file to the final refine.pdb file. - mtzchk: tool for checking MTZ file (cell parameters, space group, amplitudes and sigmas, ...) new features: - The user can override the default scratch directory (including a file-prefix) by setting the environmental variable autoBUSTER_scr. However, since the names of temporary files are now ensured to be unique (and no name clashes between different autoBUSTER jobs should occur), this will be rarely necessary (if at all). - three levels of adjusting defaults are now possible (via parameter setting in a file called .autoBUSTER): a) installation-wide in $BDG_home/autoBUSTER/bin/linux/.autoBUSTER b) user-wide in ~/.autoBUSTER c) current directory in ./.autoBUSTER - The automatic generation of a TNT sequence file (via the 'pdb2seq' command) has been improved by adding the following features: * breaks in consecutively numbered residues are detected (based on C -> +N bond length for amino-acids and O3* -> +P bond length for RNA/DNA) * connections of non-consecutively numbered residues are detected (based on C -> +N bond length for amino-acids and O3* -> +P bond length for RNA/DNA) * chains with several OXT atoms (i.e. C-terminal oxygens) are handled * detects potential modified amino-acids (residues that contain all atoms of a peptide group) * better handling of RNA/DNA models * LINK records in PDB file are now used (by default), if the atoms referred exist and the described connectivity is within a sensible bonding distance. If the two residues named in the LINK record are already connected by a standard linkage (like PEPTIDE or SUGPHOS), no additional link will be created. Also: if at least one of the atoms referenced is a metal no restraints will be generated. * inter-chain SSBOND records in input PDB file are now supported (generates SS linkages on the CHAIN card of the TNT sequence file) - A hook is provided for a user-supplied water updating routine (which will then be called instead of the built-in procedures that use PKMAPS or ARP_WATERS). improvements: - The calculation of real-space correlation values (with the 'corr' command) handles fragmented chains better. It should also not be thrown off when the order of chains and residue numbers is unusual/unexpected. - The final PDB file will carry over all relevant header records from input PDB file. The REMARK 3 header (refinement statistics) is obviously updated. - The main 'refine' command will now report the list of command line arguments to standard output. - The used set of standard dictionaries can now be changed under user-control. - The order in which restraints for non-standard residues are generated can be defined by user. By default, the dictionary is searched for in order: $BDG_home/tnt/data/msd, $BDG_home/tnt/data/ccp4, MakeTNT. - A non-standard residue for which there is a distributed dictionary available will be checked to make sure that the PDB file uses the same atom names as the distributed dictionary file. If this is not the case: a new dictionary will be generated on-the-fly (from coordinates of the best representative in the PDB file) using the program PDB2TNT from the MakeTNT toolbox. However, if the dictionary in error is a user-supplied one (given with the -l flag to the 'refine' command), an error occurs and the user is reminded to fix that external dictionary file (or the PDB file). - pdb2tnt will detect (and remove) duplicated restraints for non-standard residues (which have restraints generated on-the-fly from the PDB coordinates and are connected to other parts of the structure via some standard links, e.g. a PEPTIDE bond). - The new parameter KeepCurrentRmsBond (default = no) can be set to 'yes' if autoBUSTER should adjust the weight between X-ray and geometric term so that the final rmsd(bond) stays the same as the value for the input PDB file. - Gelly is used for some initial sanity checks: * detection of unusual short contacts (which can point to problems in restraints, TNT sequence file or PDB file). * detection of duplicated restraints (shows problem in restraints dictionary) * reporting of missing atom-atom contact distances - Generally much more initial checks at the start of an autoBUSTER job with (hopefully) meaningful feedback to the user if problems are encountered. - After the PDB file has been (internally) converted to ATOMC format (*.cor file), the atom types encoded in that new file are checked against the formfactor database. This will detect problems when translating a PDB file: * no or bogus atom type in columns 77-78 of PDB file * atom name (columns 13-16) in PDB file can't be used correctly to deduce atom type - The handling of atom and residue name for waters has been generalized and now follows the PDB standard: water atoms are named " O " and residues "HOH". - the two parameters FinalMapsNormalized (default=yes) and FinalMapsCoverPdb (default=no) can be used to specify how the 2Fo-Fc.map and Fo-Fc.map file should be generated. fixes: - Now deals better with residue names (in PDB files) that are less than 3 characters long. - The collecting of all required geometric restraints (from distributed standard dictionaries, user-supplied dictionaries or restraints created automatically on-the-fly inside autoBUSTER) now also knows about link types in addition to residues. This allows complete control of unusual linkages within the macro-molecule (attached sugars, modified amino-acids, covalently attached ligands etc). - When the starting structure shows very bad geometry (based on the value of rms(bond)): only run structure idealisation if in BUSTER-TNT mode (as opposed to the default BUSTER-GELLY-TNT mode). If structure idealisation is needed, it is highly recommended to use Gelly directly (via the 'gelly_refine' command). - Internally in autoBUSTER, the SCALE cards of a PDB file will always be removed. This is due to the lack of precision when going from orthogonal coordinates in a PDB file to the ATOMC format or *.cor file used by BUSTER, TNT and Gelly internally). The effect of not removing the SCALE cards was a slight coordinate shift - even if no positional refinement was done at all. - The program 'cor2pdb' has seen several fixes: however, since the Gelly part of BUSTER now writes a PDB file directly this tool is not used by default anymore. - When a TNT restraints dictionary needs to be generated on-the-fly (using PDB2TNT from the MakeTNT toolbox), the extraction of the best residue out of the user-supplied PDB file has been improved. For different copies of the same residue/compound it takes into account * different levels of completeness * B-factor * occupancy * alternate conformations The best occurrence of a specific residue is the one with the lowest B-factor which at the same time is the most complete. - Residues are no longer renumbered, since all programs can now deal with negative residue numbers (e.g. if a His-tag is present). ============================= Beta release of 31 Aug 2006 ============================= new features & changes: - 'refine' will now check if an autoBUSTER job was already run in same directory (or subdirectory as given with -d flag): this will trigger an error. - real-space correlations between final model and maps (using the 'corr' tool) are now calculated using the full FC/PHIC as available from BUSTER (i.e. including bulk-solvent correction). Before, only the structure factors from the actual coordinates were used. - user-defined dictionaries (-l flag to 'refine') now also accepts CCP4-formatted CIF files (which get converted internally to TNT-formatted dictionaries on-the-fly). This should make it easier to use autoBUSTER without the need of converting already available dictionaries. new tools/programs: - new tool prep_FitMAP to prepare all files necessary for running M. Brandl's ligand-fitting program (FitMAP, part of the MakeTNT toolbox) in the correct way. fixes & improvements: - improvements to the program that analyses maps and model for 'interesting' regions (ANA_PDBMAPS). This might make it easier to use it for other tasks as well. - more control on convergence when adding waters: parameter KeepAddingWatersAfterN (default=yes) will increase the total number of BIG cycles to be done as long as water update still occurs. - added 'weight_ncs' to the available settings in 'gelly_refine' - fixed a nasty typo in 'refine' (showed up on SuSE 10.1 only so far) - R/Rfree values in analyse.html are now correct again - fix in 'gelly_refine' that caused problems with GLY residues - fixes within the underlying logic of autoBUSTER refinement jobs that make it possible to run on machines even if these weren't configured as MASTERs ============================= Beta release of 13 Jul 2006 ============================= new features & changes: - uses BUSTER-GELLY-TNT, i.e. new optimiser and new geometric restraint handling - new program (ana_pdbmaps) to analyse density maps for potential ligand binding sites ('interesting' regions). This doesn't require the present of 'water' atoms anymore. This is now the default. - the minimum distance to existing atoms for placing new waters has been changed from 1.5 to 2.5 A (due to using ana_pdbmaps - see above) new tools/programs: dock_screen: initial version for general FFT-based docking, giving starting points for further refinement via torsion angles pdb2rig : simple tool to create rigid-body definitions templates seq2seq : simple script to convert ASCII sequence into TNT sequence file pdb2cor, cor2pdb: simple tools to go from/to ATOMC format gelly_refine : script to run gelly standalone, i.e. geometry-only refinement mk_o_macros.sh, mk_coot_macros.sh, mk_pymol_macros.sh: to generate scripts for graphics programs O, Coot and Pymol documentation: - up-to-date version with more examples and documentation about important flags/parameters - added documentation for additional tools - updated and enhanced documentation for 'refine' command - 'refine -h' is updated and also points to more extensive HTML documentation fixes & improvements: - handling of atom names with spaces (converted to underscore) - already present PDB header records are carried through - deal with residue names that are shorter than three characters (left or right justified) - the flag '-noWAT' can also be given an (optional) number of BIG cycles for which it should be used (e.g. skipping water-updating only for the first 3 BIG cycles) - some advanced settings can now also be given on the command line (using a parameter=value syntax) instead of placing them into a .autoBUSTER file. - added checks to avoid using FOSC/SIGFOSC and HLA-D if a MTZ file is used that is actually the output file of a previous BUSTER or autoBUSTER run - if the input PDB file needs addition of a chain ID: this is now also added to SSBOND, HELIX and STRAND cards present in the input PDB file - rigid-body defining files (given with the -RB flag) can have either the autoBUSTER-specific format or use directly the advanced Gelly-syntax - several fixes in 'pdb2seq' to have a correct output sequence file even in unusual cases (dealing with C-terminal oxygens, gaps and breaks) - no need for running 'newmachine' for every single machine the program should be run on. If the first machine the program is installed is e.g. of type Linux, then all further machines of the same type will fetch this initial configuration. So only if machines of the same type have a different setup (in respect to crystallographic software, scratch space, very different OS etc) the 'newmachine' command needs to be used. - only interesting regions of at least 50 A^3 volume are analysed (when giving the -L flag) - several fixes to allow user-control over B-factor refinement (see -B flag) - occupancy refinement should work now =================================================================== Any feedback and remarks should be send to the BUSTER developers: buster-develop@globalphasing.com ===================================================================