################################################################### # # This is the seventh SHARP/autoSHARP release in the 2.8.X/3.10.X # series: SHARP 2.8.7 and autoSHARP 3.10.7 (Dec 07 2016). It is # based on the previous 2.8.6/3.10.6 releases and available to # academic and commercial users. # # These release notes cover SHARP, the autoSHARP pipeline and the # Sushi graphical user interface. # ################################################################### # # Copyright (C) 1995-2016 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, E. de la Fortelle, C. Flensburg, # J. Irwin, P. Keller, W. Paciorek, P. Roversi, A. Sharff, # O. Smart, C. Vonrhein, T. Womack # # # References: G. Bricogne, C. Vonrhein, C. Flensburg, M. Schiltz & # W. Paciorek. (2003). Generation, representation and flow # of phase information in structure determination: recent # developments in and around SHARP 2.0. Acta Cryst. D59, # 2023-2030. # # C. Vonrhein, E. Blanc, P. Roversi & G. Bricogne # (2007). Automated structure solution with # autoSHARP. Methods Mol Biol 364, 215-30. # ################################################################### =================================================================== Changes relative to 2.8.6/3.10.6 07 Dec 2016 =================================================================== Improvements and changes (released 07 Dec 2016): * run_autoSHARP.sh: * added flag "-pdbkeep" to use input PDB file not only for finding and refining heavy-atom sites, but also use the phase information from that model during phase computation. This can be useful when dealing with weak experimental phases (and you want to include the model phases also during density modification and model building) - but could also introduce model bias! ------------------------------------------------------------------- <-- Below are the Release Notes for the previous stable release --> ------------------------------------------------------------------- =================================================================== Changes relative to 2.8.5/3.10.5 24 Mar 2016 =================================================================== Improvements and changes: * run_autoSHARP.sh: * fixes to the final reporting of result files when running the -fast option * clarified syntax of -sites flag in relation to -nsit (thanks to M. Rudolph for pointing this out) * Support for CCP4 7.0 * Handling of ARP/wARP 7.6 on systems without /usr/bin/tcsh: * ARP/wARP 7.6 scripts are started with /usr/bin/tcsh; * not all systems will have this installed (but rather /bin/tcsh or /bin/csh), e.g. CentOS5 or CentOS6; * added test for this (and enforcing subsequent building with BUCCANEER via our Long-John-Silver tool); =================================================================== Changes relative to 2.8.4/3.10.4 16 Jun 2015 =================================================================== Improvements and changes: * run_autoSHARP.sh: * create scripts for Coot to be run directly: separate scripts for the different stages of HA-detection, phasing, density-modification and model-building are available. This simplifies the viewing of results for users. * report date, directory, user name in top of the .autoSHARP file * added safety-check for unset/missing "wvlid" (wavelength identifier) and "fmid"/"smid" (amplitude/sigma) * the help message (run_autoSHARP.sh -h) now also includes an example for a Ta6Br12 cluster as heavy-atom compound. * when presenting MTZ files as part of the autoSHARP results: also report which columns should be used for various map computations. This simplifies the viewing of results in Coot based on those MTZ files. * the command-line for running "Long John Silver" (K. Cowtan's PARROT and BUCCANEER) as part of autoSHARP is better reported in a way that would allow a user to run this tool stand-alone. * the skeleton representation in the Coot scripts (for visualising electron density maps) have been improved with the help of P. Emsley. Fixes: * run_autoSHARP.sh: * safeguard against MTZ column names with ":" characters * fix bug in awk construct (triggered by non-GNU awk binary on OsX) * when starting from known positions of sites: ensure the symbolic links in the Results directory aren't confused by this. * autoSHARP: * fixed buglet that resulted in badly formatted solvent content presented in map tools for LJS results (when run through httpd interface). * depending on the ARP/wARP version used, the final PDB file was not presented in the output HTML page. * automatic interpretation of LLG residual maps was confused when multiple iterations of parameter refinement (in SHARP) and this analysis were combined with the need of f'/f" parameter refinement. * if no ARP/wARP installation is available (or not configured), keep running "Long John Silver" building tool instead of producing an error. ------------------------------------------------------------------- <-- Below are the Release Notes for the previous stable release --> ------------------------------------------------------------------- =================================================================== Changes relative to 2.8.3/3.10.3 16 Mar 2015 =================================================================== Improvements and changes: * The setup scripts have been consolidate. The installation will create two different files setup.{csh,sh} and setup-admin.{csh,sh} for two different tasks: setup.{csh,sh} : for users of the software (sets SHARP_home environment variable and puts run_autoSHARP.sh into the users PATH) setup-admin.{csh,sh} : for administrators of the software (puts commands for adding users, configuring the software and machines into the PATH) Only the setup.{csh,sh} files need to be put into a users setup e.g. via if [ -r /where/ever/sharp/setup.sh ]; then . /where/ever/sharp/setup.sh fi (for bash/sh-users) or if ( -r /where/ever/sharp/setup.csh ) then source /where/ever/sharp/setup.csh endif (for csh/tcsh users). * Changed writing of LLG residual maps from SHARP: instead of writing real and imaginary part of the structure factor it now writes amplitude and phase. This should make it much easier to load the resid.mtz file into a Coot session and show residual maps. * 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. Fixes: * Fixed hanging of interactive run_autoSHARP.sh script when no model-building was requested. * Fix in presenting results when running interactive run_autoSHARP.sh script with an initial set of sites (instead letting it do the heavy atom detection itself). * Try to recreate during installation the way CCP4 sets the environment variable CCP4_SCR including a dynamic part (user name): the resulting $SHARP_home/machines/*/ccp4.setup file(s) should now also contain this and not have the user id of the installer account hardwired. This can be switched off (to have previous default behaviour) by setting the environment variable AdjustCcp4ScrForUser to "no" before running the installation. * Fixed a bug when running autoSHARP through the CCP4i interface and declaring neither sequence nor molecular weight or number of residues. * Handle cases in autoSHARP where a site that has been refined to nearly zero occupancy by SHARP is actually on a special position and therefore didn't get recognized as a removable site during LLG residual map analysis. This resulted in running the same SHARP/LLG-analysis loop multiple times. Please also check the next block of release notes for recent changes. =================================================================== Changes relative to 2.8.2/3.10.2 04 Mar 2015 =================================================================== Improvements and changes: * A command-line tool for running autoSHARP that can easily be incorporated into the workflow. See $SHARP_home/bin/sharp/run_autoSHARP.sh -h for detailed usage help. * SHARP and SCALA2SHARP: increase maximum number of batches from 10k to 100k. This makes it possible to handle advanced data collection protocols. * Support for CCP4 6.5 (and removed support for CCP4 versions prior to 6.3.0). * Support for SHELXC version 2014/2 and SHELXD version 2013/2 * Support for ARP/wARP: - version 7.5 (changes due to changed default prefix of output filenames) - version 7.4 (changes due to changed format of refinement statistics) * New arguments to 'Long John Silver' script: -ncsrad (to set ncs-mask-filter-radius in PARROT) -free (MTZ column label for test-set flag (default = FreeR_flag) * autoSHARP will now use the same test for the 'Long John Silver' (PARROT/BUCCANEER) auto-building at lower resolution, that it already uses for the ARP/wARP path at higher resolution. If a large enough number of residues are built/docked the loop over density modification and auto-building will be stopped. * When running the non-default fast option in autoSHARP: change to use smaller steps during optimisation of solvent content since otherwise it can easily go into silly solvent content ranges for structures with exceptionally large/low solvent content. * Improved checking of SHELXC/SHELXD version to give more meaningful messages to user. * autoSHARP will now not use FHSCAL for MIR/SIR scaling: if the derivatives are higher resolution than the native it will not output those higher reflection data. It now uses SCALEIT instead for all cases. Fixes: * Fixed issue where jobs gave an erroneous warning (about solution not being good enough while it clearly was). * fixed problem with input SCA-files for structures with cell dimensions above 999.999 A * when only running model building using PARROT/BUCCANEER ("Long John Silver"), fix problem if subsequent density modification jobs came up with identical solvent content (by chance): this used to trigger an error. * added test to aStar.sh (jiffy for visualising maps/models directly from HTML file produced via CCP4i autoSHARP task) to handle SHARP_home environmental variable correctly. * fixes in 'Long John Silver' script when getting NCS operators from PARROT (however: NCS operators written by PARROT up to at least version 1.0.2 are buggy) =================================================================== Changes relative to 2.8.1/3.10.1 19 Jun 2013 =================================================================== Fixes: autoSHARP improvements: * stop complaining about spacegroup differences for cases like P1211 versus P21, ie. simply a difference in notation. * fix handling of f'/f" values when using an initial/partial model for heavy-atom substructure solution via SHARP: when used in multi-wavelength MAD the values for the second (and following) wavelengths were wrongly assigned. * give a bit more information why we would prefer the peak, infl, hrem etc nomenclature for SHELXC/D. * fixed menu for plotting maps after automatic-building with LJS tool. * support for latest SHELXC/D versions. For information regarding the latest SHELXC/D version please refer to the official documentation at http://shelx.uni-ac.gwdg.de/SHELX/ and especially http://shelx.uni-ac.gwdg.de/SHELX/changes.php * automatically translate all spaces to underscore in project name. * decision making about low-resolution model building was broken: the new long_john_silver tool was not used for data below 2.5A if the 'fast' autoSHARP option was set. =================================================================== Changes relative to 2.8.0/3.10.0 22 Oct 2012 =================================================================== Improvements and changes: * support for usage of spherical clusters in SUSHI. * new automatic-building module (long_john_silver) using BUCCANEER and PARROT by K. Cowtan. * support for SHELXD (beta) version 2011/5 in autoSHARP, including the parallelized binaries shelxd_mp and shelxd_mp64. * support for ARP/wARP 7.2 and 7.3 as well as CCP4 6.3.0 * removed support for Xfit/XtalView, Moloc and Quanta viewers * improved output and checks for the part in autoSHARP dealing with an initial/partial input model * new renaming feature within the file-upload facilty Fixes: * automatically translate all spaces to underscore in project name. * correctly fetch MTZ files (for map plotting) from GETAX (NCS-detection) runs in case of negative self-rotation angles. * deal better with low-resolution (<= 6A) data in the NCS-detection (GETAX) part: DM can't determine an appropriate scale and we need to set this by hand (as well as switching off histogram matching because of that). * avoid printing link to wrong cross-table listing in SHELXD HA detection step (when running several trials). * in SHARP, allow underscore (_) as part of project name and also a longer title (180 characters) =================================================================== Changes relative to 2.6.0/3.8.0 20 Jul 2011 =================================================================== New features: * given an initial PDB model, autoSHARP can use phases calculated from this file to detect heavy atom sites through SHARP's residual/LLG maps. This feature was present in SHARP since its beginning, but required a little bit more user intervention. Putting it into autoSHARP should make it easier to find heavy atom sites from a poor initial model. * Support for 64-bit binaries on linux. * Support for emX and pXpY network interfaces. Improvements and changes: * updated to handle also ARP/wARP 7.1 and most likely the upcoming 7.2 * clarified autoSHARP interface regarding sequence file, number of sites, wavelength and f'/f" values. * added new helper (pir2pir) for automatic detection and correction of common issues with sequence files - in particular converts a FASTA sequence into internal format * consolidate usage of PRIOR cards in the SHARP Input Editor * added spacegroups 2018 and 3018 * cleanup of different documentation links, mainly to point to official SHARP Wiki at: http://www.globalphasing.com/sharp/wiki/ * use fixed ordinate range of relative-occupancy plots of shelxd solutions for quick quality assessment * support for up to 9999 number of batches in MRF-mode * automatically set environment variables: ATOMSF, SYMINFO, SPHCLUSTER Fixes: * modified Perl code to work with latest Perl version 5.12 * fixed I41 hand inversion * made I4122 hand inversion consistent with documentation in CCP4 (reindexing.doc) * fixed map-plotting issue for ARP/wARP maps * several fixes to make PKMAPS program more robust (eq. when analysing LLG maps for additional sites) * fixed typo that prevented usage of resolution-dependent initial HAT_B value (in case no Wilson plot could be calculated for very low-resolution data) * fixup some (non-standard) space group numbers and add I2 * fixed problems in parameter refinement (SHARP hanging) due to problems in anisotropic tensor construction * fix spurious crashes when calling LRINFO(CCP4) * fix handling of multi-batch MRF cases * fix a memory leak in file_open * correct error handling when unable to write '.status' file #### 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 =================================================================== Any feedback and remarks should be send to the SHARP developers: sharp-develop@globalphasing.com ===================================================================