| BUSTER Documentation | previous |
| Appendix 1 |
| Copyright | © 2003-2020 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 authorized only pursuant to a valid written licence from GPhL. | |
| Contact | buster-develop@GlobalPhasing.com |
| Parameter [program] step affected |
default | explanation |
|---|---|---|
| AddMissingSsbondRecords [refine] PDB file checking |
"no" | Should we try and recover lost SSBOND records involving only CYS residues based on distance, angle and torsion angle? |
| AddModifiedAminoAcidToBusterSet [pdb2seq] generation of TNT sequence file |
"yes" | When automatically detecting modified-amino acids (that aren't already part of our distributed set of standard geometries): extend the Gelly set ExoticAA to include these residues. |
| AdditionalAnalysisAfterBuster [run_buster] running BUSTER |
"yes" | Report more information at end of each BUSTER run (big cycle). |
| AdjustBasedOnLinkRecords [pdb2seq] generation of TNT sequence file |
"yes" | Make use of LINK records in the input PDB file (which describe covalent bonds that are not covered by standard links like peptide groups etc). |
| AdjustBasedOnLinkRecordsAllowAltloc [pdb2seq] generation of TNT sequence file |
"yes" | When adding additional bond restraints based on LINK records in input PDB file: allow atom definitions to reference atoms in alternate conformations. |
| AdjustBasedOnLinkRecordsAngleSigma [pdb2seq] generation of TNT sequence file |
"5.0" | Default sigma value on newly generated ANGLE restraint when analysing LINK records of input PDB file. |
| AdjustBasedOnLinkRecordsBcorrelSigma [pdb2seq] generation of TNT sequence file |
"20.0" | Default sigma value on newly generated BCORREL restraint when analysing LINK records of input PDB file. |
| AdjustBasedOnLinkRecordsBondCutOffMax [pdb2seq] generation of TNT sequence file |
"2.5" | Only LINK records referring to atoms with a maximum distance of this value will be used to generate linkage and additional BOND restraint. |
| AdjustBasedOnLinkRecordsBondCutOffMin [pdb2seq] generation of TNT sequence file |
"1.2" | Only LINK records referring to atoms with a minimum distance of this value will be used to generate linkage and additional BOND restraint. |
| AdjustBasedOnLinkRecordsBondSigma [pdb2seq] generation of TNT sequence file |
"0.04" | Default sigma value on newly generated BOND restraint when analysing LINK records of input PDB file. |
| AdjustBasedOnLinkRecordsIgnoreResidues [pdb2seq] generation of TNT sequence file |
"MSE" | List of residues to ignore on LINK cards (since we know about the standard linkage for those anyway). |
| AdjustBasedOnLinkRecordsImproperSigma [pdb2seq] generation of TNT sequence file |
"5.0" | Default sigma value on newly generated IMPROPER restraint when analysing LINK records of input PDB file. |
| AdjustBasedOnLinkRecordsMetalsKeep [pdb2seq] generation of TNT sequence file |
"" | list of (space-surrounded and separated by a vertical bar "|") restraint types to keep when a metal atom is referred to as having connectivity (via a LINK record in the PDB file). By default all LINK records referring to metals are discarded: to keep e.g. the BOND and ANGLE restraint set this parameter to " BOND | ANGLE " (but this is not recommended) |
| AdjustBasedOnLinkRecordsMethod [pdb2seq] generation of TNT sequence file |
"PDB2TNT" | When defined as "LINK", a single BOND restraint will be generated between the two atoms referenced on a LINK record in the PDB file. With set to "PDB2TNT" (recommended), a more complete analysis of the two residues involved in this LINK description is done (leading to additional BOND, ANGLE etc restraints). |
| AdjustBasedOnLinkRecordsPlaneSigma [pdb2seq] generation of TNT sequence file |
"0.02" | Default sigma value on newly generated PLANE restraint when analysing LINK records of input PDB file. |
| AdjustBasedOnLinkRecordsTrigonalSigma [pdb2seq] generation of TNT sequence file |
"0.020" | Default sigma value on newly generated TRIGONAL restraint when analysing LINK records of input PDB file. |
| AdjustBoundaryResiduesInRigidBodyDefinition [refinetools] creating a rigid-body definition file |
"yes" | For a residue range in a rigid-body description: should we check that those residues are actually present and if not adjust the boundaries up and down, respectively? |
| AdjustFivePrimeEnd [pdb2seq] generation of TNT sequence file |
"yes" | Take extra steps to analyse the exact nature of the 5'-end of a RNA/DNA chain. |
| AdjustModifiedAminoAcids [pdb2seq] generation of TNT sequence file |
"YES" | When encountering unknown residues in the PDB file that have all the atoms of a normal peptide group (as encountered in amino-acid residues): should we assume those are amino-acids (yes) - even if they're N-terminal (YES)? |
| AdjustModifiedNucleotides [pdb2seq] generation of TNT sequence file |
"yes" | When encountering unknown residues in the PDB file that have all the atoms of a normal sugar-phosphate group (as encountered in DNA/RNA residues): should we assume those are DNA/RNA (yes)? |
| AdjustXrayWeightAutomatically [refine] overall refinement (BIG cycles) |
"yes" | The weight between the X-ray term (i.e. measured data) and all the geometric terms (restraints) will be adjusted automatically (see also -r and parameter KeepCurrentRmsBond). This can be switched off (no) - in which case the starting value for that weight will be used (which might not be correct). |
| AdjustXrayWeightPrecision [refine] overall refinement (BIG cycles) |
"4" | When adjusting the X-ray weight automatically based on the rms(bond) value: to what precision (i.e. number of significant digits) should we use the rms(bond) value?. |
| AdjustXrayWeightSignificantChange [refine] overall refinement (BIG cycles) |
"33" | What change (given in percent) in X-ray weight during automatic adjustment constitutes a significant change? This might also trigger an increase of the number of BIG cycles. |
| AllowBrefInRigidBody [run_buster] refinement during each BIG cycle |
"no" | Should we do B-factor refinement at the same time as doing rigid-body refinement? |
| AnaBusterIterSkip [ana_buster] after each BIG cycle |
"1" | Report statistics only for every Nth iteration (i.e. small cycle). The first and last iteration will always be reported. |
| AnaBusterVerbosity [ana_buster] after each BIG cycle |
"0" | Verbosity level for analysis after each BIG cycle: higher values print more information. |
| AnaPdbmapsCut1 [various] detection of potentially bound ligands |
"3.0" | minimum density level [rms] in the Fo-Fc map to classify a grid point belonging to a potential bound ligand |
| AnaPdbmapsCut2 [various] detection of potentially bound ligands |
"1.0" | minimum density level [rms] in the 2Fo-Fc map to classify a grid point belonging to a potential bound ligand |
| AnaPdbmapsMinVol [various] detection of potentially bound ligands |
"50.0" | minimum volume [Å] for a connected region to be classified as a potential bound ligand |
| AnaPdbmapsPadding [various] detection of potentially bound ligands |
"5.0" | safety border [Å] around the asymmetric unit during detection of connected regions |
| AnaSsbond_DistanceMax_ZnFe [ana_ssbond] Analysis to recover lost SSBOND records |
"3.0" | Any CYS residue for which there is a ZN or FE atom within that radius [A] will be ignored for further analysis of lost SSBOND records. |
| AnaSsbond_NmatchMin [ana_ssbond] Analysis to recover lost SSBOND records |
4 | Minimum number of geometric criteria that need to be fulfilled to classify a CYS-CYS disulfide bridge as SSBOND. The criteria are CYS-SG...SG-CYS bond distance, CYS-CB-SG...SG-CYS and CYS-SG...SG-CB-CYS angle as well as CYS-CB-SG...SG-CB-CYS torsion angle |
| AnaSsbond_Range_Angle [ana_ssbond] Analysis to recover lost SSBOND records |
"91.743 117.406" | limits on CYS-CB-SG...SG-CYS angle (from both sides of the disulfide bridge); default based on 99-percentile |
| AnaSsbond_Range_Distance [ana_ssbond] Analysis to recover lost SSBOND records |
"1.920 2.186" | limits on CYS-SG...SG-CYS bond distance; default based on 98-percentile |
| AnaSsbond_Range_Torsion [ana_ssbond] Analysis to recover lost SSBOND records |
"-146.076 -31.394|28.665 160.277" | limits on CYS-CB-SG...SG-CB-CYS torsion angle: two ranges edlimited by "|" need to be given; default based on 98-percentile |
| AnaVoids_ClusterSize [anavoids] |
"5.0 10.0" | If using the "ana_pdbmaps" method for defining voids (See AnaVoids_method), list of cluster sizes to associate with AnaVoids_rmss. |
| AnaVoids_dist_and [anavoids] handling of voids |
"3.00" | during detection of voids: accept negative peaks within this distance of already selected peaks |
| AnaVoids_dist_and_fac [anavoids] handling of voids |
"1.0" | during detection of voids: multiply the AnaVoids_dist_and parameter by this factor during looping over AnaVoids_rmss |
| AnaVoids_dist_not [anavoids] handling of voids |
"1.50" | detection of voids: remove peaks within this distance of the model |
| AnaVoids_dist_not_fac [anavoids] handling of voids |
"0.9" | detection of voids: multiply the AnaVoids_dist_not parameter by this factor during looping over AnaVoids_rmss |
| AnaVoids_method [anavoids] |
"orig" | one of "orig" (based on peak picking) or "ana_pdbmaps" (based on connected density regions) |
| AnaVoids_rmss [anavoids] handling of voids |
"3.5 3.0 2.5 2.0" | detection of voids: loop over these values [rms] to find negative peaks. |
| AnalyseBusterFoFc [analyse] final analysis |
"FOFCWT" | column name in final MTZ file for calculating difference Fourier maps |
| AnalyseClusterMethod [analyse] final analysis |
"new" | Which method to use for the final analysis of potential ligand-binding sites: "new" is highly recommended over "original". |
| AnalyseExtraEpdbs [analyse] final analysis |
"" | List of PDB files to use during analysis of potential ligand-binding sites (on top of the automatically found or user-defined ones). |
| AnalyseFivePrimeEnd [pdb2seq] generation of TNT sequence file |
"yes" | Check if residues defined as [d]5'END contain also the atoms of the phosphate group - which would require change of linkage to [d]5'PEND. |
| AnalyseForModifiedResidues [pdb2seq] generation of TNT sequence file |
"yes" | Should we analyse for modified amino-acids? |
| AnalyseGellySanityCheckForDuplicateBonds [run_buster] refinement during each BIG cycle |
"yes" | After running the initial sanity check with Gelly: should we analyse the report to see if Gelly encountered duplicated bond restraints? |
| AnalyseLinkRecords [pdb2seq] generation of TNT sequence file |
"yes" | Should we analyse the LINK records found in the input PDB file when generating the TNT sequence file? |
| AnalysePictureCarve [analyse] final analysis |
"3.0" | When generating pictures of potential binding sites: radius around binding-site describing PDB file for density. |
| AnalysePictureLarge [analyse] final analysis |
"800,800" | Size of large pictures generated by Pymol (in pixels) |
| AnalysePictureLevel_2FoFc [analyse] final analysis |
"1.0" | Density level [rms] for 2Fo-Fc maps when creating pictures. |
| AnalysePictureLevel_FoFc [analyse] final analysis |
"3.0" | Density level [rms] for Fo-Fc maps when creating pictures. |
| AnalysePictureSmall [analyse] final analysis |
"100,100" | Size of small pictures generated by Pymol (in pixels) |
| AnalyseVoids [refine] overall refinement (BIG cycles) |
"yes" | Should we try and detect (and describe) pockets on the inside of the molecule, that are probably not accessible to the bulk-solvent region (and should therefore be kept empty)? |
| AnalyseVoidsAlways [refine] overall refinement (BIG cycles) |
"no" | Usually, the analysis of empty pockets (in the interior of the molecule) is not done at every BIG cycle. |
| AnalyseVoidsLast [refine] overall refinement (BIG cycles) |
"yes" | Should the analysis of empty pockets (in the interior of the molecule) be done at the very last BIG cycle? |
| AnalyseVoidsStopOnError [refine] |
"no" | Should we stop when the analysis of voids gave an error? The default ("no") will not stop - better to give a warning and finish with the normal set of files (but without void-correction). |
| AssumePdbFromRefinerCorrect [refine] overall refinement (BIG cycles) |
"yes" | Is the PDB file coming out of the refinement step correct (and doesn't need post-processing)? |
| AutomaticFormfactorCorrection [run_buster] |
"no" | When encountering elements with a significant (calculated) f' value at the given wavelenght: adjust formfactors for those elements(see also wavelength parameter). Usually, the wavelength is taken from the MTZ file header (which should be correct if data was processed e.g with autoPROC) |
| AutomaticFormfactorCorrectionAnalyse [run_buster] |
"yes" | Analyse elements for possible formfactor correction (only AutomaticFormfactorCorrection set to "yes" will actually perform this correction). |
| AutomaticRestrictLowres [refine] overall refinement (BIG cycles) |
"yes" | Should we try and detect problems with the low-resolution data by analysing the correlation CC(Fo,Fc) and restrict the lowest resolution accordingly? |
| AutomaticRestrictLowresBinCut [refine] overall refinement (BIG cycles) |
"0.5" | During analysis of low-resolution CC(Fo,Fc): what fraction of the lowest resolution bin should be excluded? |
| AutomaticRestrictLowresCcCut [refine] overall refinement (BIG cycles) |
"0.0" | During analysis of low-resolution CC(Fo,Fc): a value below this cut-off triggers restriction of the low-resolution limit. |
| AutomaticRestrictLowresFromCycle [refine] overall refinement (BIG cycles) |
"2" | During analysis of low-resolution CC(Fo,Fc): after which BIG cycle should the analysis be started? |
| BelieveAllTorsionRestraints [dic2tnt] |
"yes" | always use torsion angle restraints as is (if set to "no" only those from - usually - Grade dictionaries will be active) |
| BusterAnisoSet [run_buster] |
"Empty" | explicitly set the type of atoms that should be refined with individual ADPs |
| BusterAnoFourier [refine] |
"yes" | compute and analyse anomalous difference Fourier map (if anomalous differences are present in input MTZ file) |
| BusterAnoFourierIncludeInFinalMtz [refine] |
"yes" | include anomalous data into final output MTZ file |
| BusterAnoFourierKeepMap [refine] |
"no" | keep the anomalous Fourier map (e.g. for visualisation in Coot) |
| BusterCrdMlscalKeyword [run_buster] refinement during each BIG cycle |
"MLSCAL" | Used to fine-tune scaling algorithm in BUSTER. |
| BusterCreateCif [refine] |
"yes" | create deposition-ready PDBx/mmCIF files |
| BusterEarlyLate [refine] |
"yes" | compute and analyse F(early)-F(late) difference Fourier radiation damage detection maps (if the required columns are present in input MTZ file, e.g. from processing with autoPROC) |
| BusterEarlyLateAnalyse [refine] |
"yes" | analyse the F(early)-F(late) difference Fourier radiation damage detection maps relative to the current model - to (potentially) highlight the atoms/residues impacted by radiation damage |
| BusterEarlyLateIncludeInFinalMtz [refine] |
"yes" | include map coefficients into final MTZ file (so F(early)-F(late) difference Fourier radiation damage detection maps can be shown in Coot) |
| BusterEarlyLateKeepMap [refine] |
"no" | also keep the F(early)-F(late) difference Fourier radiation damage detection map itself |
| BusterExe [run_buster] refinement during each BIG cycle |
"$BDG_bin/buster" | Full path of BUSTER binary to use. |
| BusterExpdta [harvest] |
"X-RAY DIFFRACTION" | to descripe the EXPDTA item |
| BusterExtraArgs [run_buster] refinement during each BIG cycle |
"" | Extra command-line arguments for BUSTER. Most command-line flags and options one would want to pass to the gelly module of BUSTER can be given directly. |
| BusterFreeFlagValue [run_buster] refinement during each BIG cycle |
"0" | Set value of FreeR_flag (FREFLG) to use as test set. |
| BusterGellyKwd [run_buster] refinement during each BIG cycle |
"GELLY=1" | Used to fine-tune interaction of BUSTER with Gelly. |
| BusterReportCmd [refine] |
"buster-report" | if BusterReportRun is set to "yes", which command to use for running buster-report (see also BusterReportDir). The complete command will be $BusterReportCmd -d $subdir -dreport $BusterReportDir. |
| BusterReportDir [refine] |
"" | Into which directory should the buster-report output be written? If left empty, the default will be "report" or "$subdir.report" (where $subdir is set with the "refine -d" argument). The usual way of switching on generation of a "buster-report" run at the end will be with "refine -report -d XYZ ..." which will create "XYZ.report" at the end. |
| BusterReportRun [refine] |
"no" | Determines if "buster-report" should be run or not; usually set via the "refine -report" flag. |
| BusterResolutionLimitHighres [run_buster] |
"yes" | high resolution limit can't be higher than actual data |
| BusterResolutionLimitLowres [run_buster] |
"yes" | low resolution limit can't be higher than actual data |
| BusterRigidBodyBimpfFrgLowResCut [run_buster] refinement during each BIG cycle |
"4.0" | Resolution cut-off above which the imperfection B-factor of the fragment will not be refined when running rigid-body refinement. |
| BusterRigidBodyBimpfFrgNeverRefine [run_buster] refinement during each BIG cycle |
"no" | Should the imperfection B-factor of the fragment never be refined during rigid-body refinement? |
| BusterSetDFc [refine] |
"yes" | perform DFc completion (for 2mFo-DFc map coefficients) |
| BusterSetDFcAlwaysExpand [refine] |
"yes" | always expand the input MTZ file to have a full/complete set of indices right to the highest resolution limit (i.e. no need for the user to "uniqueify" the input MTZ file beforehand) |
| BusterSetDFcAnisoFill [aB_deposition_prep] |
"_aniso-fill" | column-name for DFc completion (anisotropic based on STARANISO analysis) |
| BusterSetDFcFlag [Ligand/Refine/refine.sh] |
"SA_flag" | name of flag column from STARANISO |
| BusterSetDFcHighRes [refine] |
"0" | do not change the high resolution end (can only contract) |
| BusterSetDFcIsoFill [aB_deposition_prep] |
"_iso-fill" | column-name for DFc completion (isotropically) |
| BusterSetDFcLowRes [refine] |
"9999.9" | extend lower resolution limit to include all low-resolution indices |
| BusterSmallFootprint [refine] |
"yes" | remove as much files as possible |
| ColumnName_FreeR_flag [refine] Start of refinement |
"FreeR_flag" | Column name in MTZ file for test-set defining flag. |
| ColumnName_FreeR_flag_allowed [refine] Start of refinement |
" I FreeR_flag| I FreeRflag| I FREE| I R-free-flags" | List (|-separated) of allowed column names (including column type) for test set flag. |
| Cor2Pdb_FixAtomNamesOfResidues [cor2pdb] converting TNT-formatted cor file to PDB |
"FAD|NAP|NAI|COA|NDP|NAD|AP5|CAA|NAH|ACO" | for which residues should we try and fix the atom names? |
| Cor2Pdb_FixHydrogenAtomNames [cor2pdb] converting TNT-formatted cor file to PDB |
"yes" | Should we try and fix hydrogen atom names? |
| Cor2Pdb_FixResidueNameRightJustified [cor2pdb] converting TNT-formatted cor file to PDB |
"yes" | When generating the residue name - should it be right-justified in output PDB file? |
| Cor2Pdb_RenameWat [cor2pdb] converting TNT-formatted cor file to PDB |
"yes" | Should we rename incoming waters to a common atom/residue naming scheme? |
| CorrEnforceSfcalc [corr] calculation of real-space correlations |
"no" | by default, "corr" will re-use existing FC/PHIC columns in the input MTZ file. With this parameter set to "yes" it will recalculate structure factors from the given PDB file instead. |
| CorrHighResScale [corr] calculation of real-space correlations |
"1.0" | To get a finer grid in maps used for calculating real-space correlations, set this to a value greater than one. |
| CorrMainChainAtoms [corr] |
" N | CA | C | O " | bar-separated list of atom names (in standard PDB format, ie. 4 characters to match against columns 13-16 of ATOM/HETATM records) to represent main-chain atoms of residues in the combined list of CorrMainChainResidues+CorrMainChainResiduesAdd-CorrMainChainResiduesDel. |
| CorrMainChainReset [corr] |
"no" | Should we ensure that only amino-acid residues (as defined in CorrMainChainResidues) will have atoms (defined in CorrMainChainAtoms) classified as main-chain? All other atoms (or atoms of other residues) will be classified as side-chain atoms. |
| CorrMainChainResidues [corr] |
"ALA|CYS|ASP|GLN|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLU|ARG|SER|THR|VAL|TRP|TYR|MSE" | bar-delimited list of residue names that can have main-chain atoms (as defined in CorrMainChainAtoms); requires strings of 3 characters (columns 18-20 in ATOM/HETATM records). |
| CorrMainChainResiduesAdd [corr] |
"" | bar-delimited list of additional residues that ca have main-chain atoms (see CorrMainChainResidues). |
| CorrMainChainResiduesDel [corr] |
"" | bar-delimited list of residues to exclude from main-chain containing residues (see CorrMainChainResidues and CorrMainChainResiduesAdd). |
| CorrMtvPrefix [corr] calculation of real-space correlations |
"CC" | Prefix for files created by real-space correlation tool. |
| CorrRemapRes [corr] |
"yes" | remap residues to ensure the SFALL/OVERLAPMAP toolchain can handle the existing chain identifiers plus residue numbers. |
| CorrRunSeparateChains [corr] calculation of real-space correlations |
"no" | When calculating real-space correlation coefficients: should we run separate steps for each chain? This might be needed for large projects (since otherwise the bookkeeping of grid points to residues overflows). |
| CuKa [run_buster] |
"1.54180" | default wavelength (if wavelength is unset and MTZ header contains a value of 0.0) |
| DicFromPdbAllAtomsInBond [ab_pdb2tnt] generation of TNT restraints |
"yes" | Should we check that any restraints dictionary generated from current PDB coordinates has each atom (of that residue/group) in at least one BOND restraint? |
| DiffFourier_CompareCut [diff_fourier] |
"1.0" | distance (including symmetry-operator) between peaks found in difference Fourier map and (optional) reference PDB file. |
| DoCleanupAfterBuster [run_buster] refinement during each BIG cycle |
"yes" | Should BUSTER remove several less important or temporary files after each BIG cycle? |
| DoCleanupAfterBusterCleanHtml [run_buster] refinement during each BIG cycle |
"no" | When removing various files (see above): should we attempt to adjust the corresponding HTML files to avoid dangling links? |
| DoRigidIfCellDiffer [refine] overall refinement (BIG cycles) |
"yes" | If the cell parameters of MTZ and PDB file differ significantly: should BUSTER perform an initial rigid-body refinement automatically? |
| DoWaterRemoveDeleted [maptools] various steps involving maps |
"yes" | When updating waters: should newly placed waters be removed if they're too close to waters that have been removed at earlier cycles? This is an attempt of avoiding adding/deleting the same 'waters' over and over again. |
| ExcludeBadContacts [run_buster] refinement during each BIG cycle |
"" | Shortcut to exclude specific contacts (via TNT EXCLUDE card - see http://www.uoxray.uoregon.edu/tnt/guide/node16.html). The syntax is a ";"-separated list of valid EXCLUDE cards. |
| ExcludeResiduesFromFetching [ab_pdb2tnt] |
"" | (|-separated) list of residues we will exclude from fetching dictionaries (because they are already dealt with by linkages) |
| ExcludeResiduesFromSequence [pdb2seq] generation of TNT sequence file |
"HOH|OXY" | Residue names (bar-separated list) for which no RESIDUE card should be generated when creating the TNT sequence file with pdb2seq. |
| ExcludeWatersCloseDist [pkmapstools] water updating |
"2.5" | Minimum distance from existing atoms a newly found water needs to have. |
| ExcludeWatersCloseMapDiss [pkmapstools] water updating |
"3.0 2.5 2.0 5.0" | A list of distances from existing atoms a newly found water needs to have. |
| ExcludeWatersCloseMapRmss [pkmapstools] water updating |
"6.0 5.0 4.0 0.0" | A list of cut-off levels [rms] for picking new waters. |
| ExcludeWatersClusterCloseDist [refine] |
"2.5" | After having defined an "interesting" region (eq. density regions represented by clusters for potential ligands), remove waters closer than this distance (in Å) to those regions. |
| FftMapMinHighResLimit [prep_rhofit/refine] |
"1.5" | maps will be calculated with a high-resolution limit of 1.5A (even if the data doesn't go that far): this basically defines the grid. |
| FinalMapsCoverPdb [refine] presentation of results |
"no" | Should the final maps (Fo-Fc.map and 2Fo-Fc.map) cover the final PDB file (refine.pdb)? |
| FinalMapsNormalized [refine] presentation of results |
"yes" | Should the final maps (Fo-Fc.map and 2Fo-Fc.map) be normalized to have a mean of zero and a rms of one? |
| FinalResultsLinkOnly_mtz [refine] presentation of results |
"no" | Should we create a symbolic link for the final MTZ file (refine.mtz) instead of copying it? |
| FixXyz [various] refinement |
"no" | should all atom positions (X, Y and Z coordinates) be fixed? |
| FormfactorCorrection [run_buster] refinement during each BIG cycle |
"" | Space separated list of <AtomType>:<Fprime> pairs, describing the actual f' value (<Fprime>) of a given atom (<AtomType>). This way one could e.g. adjust the formfactor calculation when data was collected at the absorption edge of an element. |
| FormfactorCorrectionMinDiff [run_buster] |
"0.1" | minimum difference between current formfactor and corrected formfactor (given wavelength) before a warning will be issued and/or automatic correction will be applied. |
| FixPotentiallyWrongEndTargetsForOxt [pdb2seq] generation of TNT sequence file from PDB file |
"no" | Should we try and fix potentially wrong AEND/ENDA targets for C-terminal oxygens (OXT)? |
| FixedSolventScales [run_buster] during each BIG cycle |
"no" | Should we keep the solvent scales at fixed values? This uses some simple, resolution-dependent values based on analysing refinements of a large variety of deposited PDB structures (see below) |
| FixedSolventScales_K_SOLV [run_buster] during each BIG cycle |
(calculated with formulae below) | Solvent scale factor |
| FixedSolventScales_K_SOLV_m [run_buster] during each BIG cycle |
"0.163" | For calculating K_SOLV = m*HighRes + b |
| FixedSolventScales_K_SOLV_b [run_buster] during each BIG cycle |
"0.456" | For calculating K_SOLV = m*HighRes + b |
| FixedSolventScales_B_SOLV [run_buster] during each BIG cycle |
(calculated with formulae below) | Solvent scaling B-factor |
| FixedSolventScales_B_SOLV_m [run_buster] during each BIG cycle |
"32.56" | For calculating B_SOLV = m*HighRes + b |
| FixedSolventScales_B_SOLV_b [run_buster] during each BIG cycle |
"-31.91" | For calculating B_SOLV = m*HighRes + b |
| FixedSolventScales_B_IMPF_SOLV [run_buster] during each BIG cycle |
(calculated with formulae below) | Solvent scaling imperfection B-factor |
| FixedSolventScales_B_IMPF_SOLV_m [run_buster] during each BIG cycle |
"-34.34" | For calculating B_IMPF_SOLV = m*HighRes + b |
| FixedSolventScales_B_IMPF_SOLV_b [run_buster] during each BIG cycle |
"114.68" | For calculating B_IMPF_SOLV = m*HighRes + b |
| FixedSolventScales_K_IMPF_SOLV [run_buster] during each BIG cycle |
1.0 | Solvent imperfection scale factor |
| GemmiConvertArg [aB_deposition_prep] |
"--skip-category=entity_poly." | |
| GemmiConvertBlockName [aB_deposition_prep] |
"BUSTER_model" | |
| GemmiMtz2cifArg [aB_deposition_prep] |
"--skip-empty --no-comments" | |
| GeometryWeight_angle [run_buster] refinement during each BIG cycle |
"2.0" | Weight for geometric ANGLE restraints. |
| GeometryWeight_bcorrel [run_buster] refinement during each BIG cycle |
"20.0" | Weight for geometric BCORREL restraints. Please note that in "gelly_refine" the default is set to zero. |
| GeometryWeight_bond [run_buster] refinement during each BIG cycle |
"2.0" | Weight for geometric BOND restraints. |
| GeometryWeight_chiral [run_buster] refinement during each BIG cycle |
"5.0" | Weight for geometric CHIRAL restraints. |
| GeometryWeight_contact [run_buster] refinement during each BIG cycle |
"5.0" | Weight for non-bonded CONTACT term restraints. |
| GeometryWeight_defaults [run_buster.sh] refinement during each BIG cycle |
"2.0 2.0 0.0 2.0 0.0 5.0 2.0 5.0 5.0 20.0 50.0 4.0" | list of defaults for geometric restraints (same order as GeometryWeight_names) |
| GeometryWeight_ideal [run_buster] refinement during each BIG cycle |
"2.0" | Weight for geometric IDEAL distances. |
| GeometryWeight_improper [run_buster] refinement during each BIG cycle |
"0.0" | Weight for geometric IMPROPER term restraints. |
| GeometryWeight_names [run_buster] refinement during each BIG cycle |
"bond angle improper torsion pseudo plane trigonal chiral contact bcorrel ncs ideal" | identifier for various geometric restraints (same order as GeometryWeight_defaults) |
| GeometryWeight_ncs [run_buster] refinement during each BIG cycle |
"50.0" | Weight for NCS restraints. Please note that in "gelly_refine" the default is set to 4.0. |
| GeometryWeight_plane [run_buster] refinement during each BIG cycle |
"5.0" | Weight for geometric PLANE restraints. |
| GeometryWeight_pseudo [run_buster] refinement during each BIG cycle |
"0.0" | Weight for geometric PSEUDO term restraints. |
| GeometryWeight_torsion [run_buster] refinement during each BIG cycle |
"2.0" | Weight for geometric TORSION restraints. |
| GeometryWeight_trigonal [run_buster] refinement during each BIG cycle |
"2.0" | Weight for geometric TRIGONAL restraints. |
| HarvestCalculateDpi [harvest] creation of REMARK 3 section |
"all" | Which "diffraction precision index" (DPI) values to calculate. |
| IncludeNonStandardInitialRemarkSectionInFinalPdb [refine] creation of final PDB file |
"yes" | Should we include a non-standard REMARK header with job-information into the final PDB file? |
| InitialiseBiso [refine] overall refinement (BIG cycles) |
"no" | Should we initialise the atomic B-factor to a certain value before refinement? One of "yes", "no", "wilson" or a value (e.g. "40.0") |
| InitialiseBisoFallback [refine] overall refinement (BIG cycles) |
"20.0" | If the original intended method (see InitialiseBiso) of resetting the atomic B-factor failed: what value should we use as a fallback? |
| KeepAddingWatersAfterN [refine] overall refinement (BIG cycles) |
"yes" | After the initial number of BIG cycles have been reached but waters are still added: should we keep going until no further significant number of waters are added? |
| KeepAdjustingXrayWeightAfterN [refine] after each BIG cycle |
"no" | Should we increase the number of BIG cycles if the X-ray weight is still adjusted significantly? |
| KeepCurrentRmsBond [refine] overall refinement (BIG cycles) |
"no" | Try to adjust the X-ray weight (from its starting value) to keep the rmsd(bond) at the value of the input PDB file? |
| KeepHydrogens [various] handling of user-supplied PDB file |
"yes" | should hydrogen atoms be kept? |
| KeepHydrogensBabslv [run_buster] handling of PDB file for bulk solvent masking |
"no" | should hydrogen atoms be kept when creating the bulk-solvent mask? |
| KeepHydrogensNup [run_buster] handling of PDB file for non-uniform prior |
"no" | should hydrogen atoms be kept when creating the non-uniform prior mask? |
| KeepZeroOcc [various] handling of user-supplied PDB file |
"yes" | should atoms with an occupancy of zero be kept? |
| KeepZeroOccBabslv [run_buster] handling of PDB file for bulk solvent masking |
"no" | should atoms with an occupancy of zero be kept when creating the bulk-solvent mask? |
| KeepZeroOccNup [run_buster] handling of PDB file for non-uniform prior |
"no" | should atoms with an occupancy of zero be kept when creating the non-uniform prior mask? |
| LastCycleBsolv2Bmiss [run_buster] refinement during each BIG cycle |
"no" | When using missing atoms in the last cycle: should the B-factor for this contribution be initialized to the current value of the bulk solvent? |
| LastCycleKsolv2Kmiss [run_buster] refinement during each BIG cycle |
"no" | When using missing atoms in the last cycle: should the scale factor for this contribution be initialized to the current value of the bulk solvent? |
| LastCycleRefineBmiss [run_buster] refinement during each BIG cycle |
"no" | Should the B-factor of missing atoms be refined at the last cycle (if the missing atoms channel is used at all)? |
| LastCycleRefineKmiss [run_buster] refinement during each BIG cycle |
"no" | Should the scale factor of missing atoms be refined at the last cycle (if the missing atoms channel is used at all)? |
| LigandDescribingPdbMethod [refine] overall refinement (BIG cycles) |
"new" | Which method to use for describing any potential ligand binding site: "new" is highly recommended over "original". |
| MacroReport [refine] |
"no" | Should we report additional information when reading/processing macros (mainly useful for debugging)? |
| MaxAllowedCNDistanceInSeq [pdb2seq] generation of TNT sequence file |
"2.0" | If C-N distances (between amino-acid residues considered to be connected via a PEPTIDE) are above this we treat is as a break. |
| MaxAllowedOPDistanceInSeq [pdb2seq] generation of TNT sequence file |
"2.5" | If O3*-P distances (between RNA/DNA residues considered to be connected via a dSUGPHOS/SUGPHOS) are above this we treat is as a break. |
| MinAllowedCNDistanceInSeq [pdb2seq] generation of TNT sequence file |
"1.65" | If C-N distances (between amino-acid residues considered to be not connected, i.e. a BREAK) are below this we treat is as a peptide. |
| MinAllowedOPDistanceInSeq [pdb2seq] generation of TNT sequence file |
"2.0" | If O3*-P distances (between RNA/DNA residues considered to be not connected, i.e. a BREAK) are below this we treat is as a dSUGPHOS/SUGPHOS. |
| MissingAtomsBfac [run_buster] running BUSTER |
"150.0" or Wilson-B times factor | Which B-factor should we assign to the declared missing atoms (if the missing atom channel is being used)? The default is to use the Wilson B-factor times the MissingAtomsBfacFactor. If no Wilson B-factor can be calculated, use 150.0 instead. |
| MissingAtomsBfacFactor [run_buster] running BUSTER |
"1.25" | Factor to apply to MissingAtomsBfac: the idea is that any missing part is likely to have a higher B-factor than the average atom. |
| MissingAtomsBfacSigma [run_buster] running BUSTER |
"15.0" or Wilson-B times factor | Which sigma should the B-factor for the declared missing atoms have (if the missing atom channel is being used)? The default is to use the Wilson B-factor times the MissingAtomsBfacSigmaFactor. If no Wilson B-factor can be calculated, use 15.0 instead. |
| MissingAtomsBfacSigmaFactor [run_buster] running BUSTER |
"0.125" | Factor to apply to MissingAtomsSigmaBfac |
| Mtv2PngGeom [mtv2png] |
"1200x900" | |
| MtzChk_MaxNumToPrint [mtzchk] Initial check of input MTZ file |
"10" | How many reflections/lines to print (if needed)? |
| Mtztools_FreeRflag_FrcMax [mtztools] Handling MTZ file |
"0.10" | Maximum fraction of available reflections to assign to test-set (if a new test-set needs to be created). |
| Mtztools_FreeRflag_FrcMin [mtztools] Handling MTZ file |
"0.05" | Minimum fraction of available reflections to assign to test-set (if a new test-set needs to be created). |
| Mtztools_FreeRflag_NumAim [mtztools] Handling MTZ file |
"1000" | Ideally, this number of reflections should be placed into a newly created test-set (if required). |
| MxlcycCutBuster [refine] overall refinement (BIG cycles) |
"0.75" | When reducing the number of necessary small refinement cycles (while using the old TNT minimizer - it has no effect with the new Gelly minimizer): use this factor to reduce (or increase) the number of small cycles for the next BIG cycle. |
| NeverGenerateDictionary [run_buster] refinement within each BIG cycle |
"yes" | Disable the (strongly non-recommended) option to produce ligand dictionaries based on the current conformation of the ligand in the model |
| NmissMinimumFrac [run_buster] refinement within each BIG cycle |
"0.05" | Minimum fraction (relative to number of atoms of current PDB file) below which the missing atom channel will not be used. |
| NmissMinimumFracWarnOnly [run_buster] refinement within each BIG cycle |
"no" | Should we only warn (but keep using it) if the number of atoms defined as missing atom channel drops below NmissMinimumFrac? |
| NoOverallBanisoRefinement [run_buster] refinement during each BIG cycle |
"no" | If set to yes (and no previous CRD.scale file is present): set the NOBREF flag in BUSTER |
| NonStandardInitialRemarkSectionCard [refine] Generation of final PDB file |
"REMARK" | string to be used in the BUSTER-generated, non-standard PDB header part (at top of refine.pdb) |
| NonStandardInitialRemarkSectionDelimiter [refine] Generation of final PDB file |
"yes" | should we create the delimiting lines to enclose the BUSTER-generated, non-standard PDB header part (at top of refine.pdb) |
| PassThroughArgs [refine] overall refinement (BIG cycles) |
"-autoncs -autoncs_weight:n -autoncs_noprune -target:f -target_weight:n -dlim:n -glim:n -sim_swap_equiv -sim_swap_equiv_plus -screen:i -screen_sigma:n -verbose:i -verbose_set -type:s -max:i -gelly_fn -tnt_fn -tnt_range_match -torsharm -updatedist:n -special_tnt -special_dist:n -keeppdb:i" | List of command-line options/flags passed through directly to the gelly module of BUSTER |
| PassThroughArgsUser [refine] overall refinement (BIG cycles) |
"" | List of additional (user definable) command-line options/flags passed through directly to the gelly module of BUSTER |
| Pdb2Dpi_NparPerAtom [pdb2dpi] |
"4" | default number of refined parameters per atom (assuming X, Y, Z and B refinement); used in DPI calculation after Cruickshank. |
| Pdb2OccLim [pdb2occ] |
"1.0" | consider atoms with occupancy below this limit |
| Pdb2OccRes [pdb2occ] |
"" | space-delimited list of residue names that should be considered for generation of occupancy-refinement cards; can be used to switch on occupancy refinement for single compounds. |
| Pdb2Tls_AdjustBorderResidueNumbers [pdb2tls] creating TLS description from PDB file |
"yes" | If there is a residue range in the REMARK 3 section of the PDB file: should we check and adjust the bordering residues if those don't exist? |
| Pdb2Tls_AutomaticDefinition_EachMacroMolChain_usecurly [pdb2tls] creating TLS description from PDB file |
"yes" | When creating an automatic TLS set definition: use the curly-bracket notation? |
| Pdb2Tls_AutomaticDefinition_OnePerChain_SkipBreaks [pdb2tls] creating TLS description from PDB file |
"no" | When creating an automatic TLS set definition: how to deal with breaks in the sequence? |
| Pdb2Tls_AutomaticDefinition_OnePerChain_minatm [pdb2tls] creating TLS description from PDB file |
"100" | When creating an automatic TLS set definition: how many non-water atoms does a chain need to have to be considered as a TLS group? |
| Pdb2Tls_AutomaticDefinition_type [pdb2tls] creating TLS description from PDB file |
"EachMacroMolChain" or "OnePerChain" | When creating an automatic TLS set definition: what method to use. Default = EachMacroMolChain |
| Pdb2Tls_FormatType [pdb2tls] |
"BUSTER" | |
| Pdb2Tls_HeaderDefinition_useval [pdb2tls] creating TLS description from PDB file |
"yes" | If a REMARK 3 section describing TLS is found: should we also make use of the values reported in there? |
| PdbChk_AdditionalChecksToDo [pdbchk] initial checking of PDB file |
"" | Additional tests to perform in pdbchk (after the defualt list of checks). For user-provided programs the full path is required. |
| PdbChk_AtomNameUnsupportedCharacters1 [pdbchk] initial checking of PDB file |
"#!" | Which characters are not allowed as part of the atom name. |
| PdbChk_AtomNameUnsupportedCharacters2 [pdbchk] initial checking of PDB file |
"AB" | Substitute characters that are not allowed as part of the atom name by those characters (see above). |
| PdbChk_AtomNamesAgainstStandardRestraintsExclude [pdbchk] initial checking of PDB file |
"^OXT$|^H$|^H[HZGABDE0-9]|^[0-9HA]H|^HT[0-9]$" | When testing atom names against standard restraints dictionaries: exclude those atoms. |
| PdbChk_AtomNamesAgainstStandardRestraintsWarning [pdbchk] initial checking of PDB file |
"^O3P$" | When testing atom names against standard restraints dictionaries: only produce warning for those atoms |
| PdbChk_ChecksNotToDo [pdbchk] initial checking of PDB file |
"" | Selected tests not to perform in pdbchk. |
| PdbChk_FixAtomNamesOfResidues [pdbchk] initial checking of PDB file |
"FAD|NAP|NAI|COA|NDP|NAD|\ AP5|CAA|NAH|ACO" |
Adjust the atom names of those residues (mostly to have correct alignment in columns 13-16). |
| PdbChk_InitialChecksToDo [pdbchk] |
"" | space-separated list of checks to do before the default checks defined in pdbchk. For user-provided programs the full path is required. |
| PdbChk_MaxNumToPrint [pdbchk] initial checking of PDB file |
"10" | Maximum number of lines/messages to print during warning/error messages. |
| PdbChk_MaximumCellAngle [pdbchk] initial checking of PDB file |
"155.000" | Maximum allowed cell angle (on CRYST1 record) |
| PdbChk_MaximumCellEdge [pdbchk] initial checking of PDB file |
"9999.999" | Maximum allowed cell edge (on CRYST1 record) |
| PdbChk_MaximumCellVolume [pdbchk] initial checking of PDB file |
"10000000000.00" | Maximum allowed cell volume (from CRYST1 record) |
| PdbChk_MinimumCellAngle [pdbchk] initial checking of PDB file |
"25.000" | Minimum allowed cell angle (on CRYST1 record) |
| PdbChk_MinimumCellEdge [pdbchk] initial checking of PDB file |
"1.010" | Minimum allowed cell edge (on CRYST1 record) |
| PdbChk_MinimumCellVolume [pdbchk] initial checking of PDB file |
"10.00" | Minimum allowed cell volume (from CRYST1 record) |
| PdbChk_PossibleChainIds [pdbchk] initial checking of PDB file |
"ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890" | String containing all possible and supported chain identifiers. |
| PdbChk_RecordFormats [pdbchk] initial checking of PDB file |
"CRYST1 ATOM HETATM" | List of PDB records for which a detailed format-analysis is done. |
| PdbChk_TooShortRecordsList [pdbchk] initial checking of PDB file |
"HEADER;66: REVDAT;66: DBREF ;68: HELIX ;76: SSBOND;72: LINK ;72: HYDBND;72: SLTBRG;72: CISPEP;59: SITE ;61: ORIGX1;55: ORIGX2;55: ORIGX3;55: SCALE1;55: SCALE2;55: SCALE3;55: MTRIX1;60: MTRIX2;60: MTRIX3;60: MODEL ;14: ATOM ;80: SIGATM;80: ANISOU;80: SIGUIJ;80: HETATM;80: TER ;27: ENDMDL;6: CONECT;61: END ;6" |
List of records (and expected lengths) to make sure all records have correct minimum length. |
| PdbChk_WrongReferenceToCoordinateRecordError [pdbchk] initial checking of PDB file |
"SSBOND|LINK " | List of (bar-delimited) PDB records for which a reference to non-existing coordinate record will trigger an error. |
| PdbStandardResidues [pdbchk] initial checking of PDB file |
"ALA|ARG|ASN|ASP|ASX|CYS|GLN|GLU|GLX|GLY|\ HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|TRP|\ TYR|UNK|VAL| A| +A| C| +C| G| +G| I|\ +I| T| +T| U| +U" |
List of standard residues in PDB files ("|"-separated, 3 character wide). |
| Pdbtools_OccMax [pdbtools] |
"1.00" | maximum allowed occupancy in various pdbtools tasks |
| Pdbtools_OccMin [pdbtools] |
"0.00" | minimum allowed occupancy in various pdbtools tasks |
| RemoveOldNonStandardInitialRemarkSection [refine] creation of final PDB file |
"yes" | Should we remove any pre-existing BUSTER generated non-standard REMARK records from the input PDB file? |
| RemoveScaleCardsFromPdb [various] conversion from PDB to ATOMC format and back |
"yes" | To make sure that the conversion between orthogonal and fractional coordinates is done with the correct precision: make sure that any SCALE record is removed from the PDB file before conversion. |
| RenumberIfBelow [run_buster] refinement during each BIG cycle |
"-999" | Residues in the input PDB file that have numbers below this will be renumbered. |
| ReportHostname [refine] |
"yes" | Should we report basic information about host, user, date etc right at the top of standard output? |
| ReuseExcludeCards [refine] |
"yes" | From BIG cycle 2 onwards, keep using the same set of EXCLUDE cards (automatically generated during the first BIG cycle to prevent bad contact terms between atoms across symmetry elements). |
| ReuseFormfactorFile [refine] |
"yes" | From BIG cycle 2 onwards, keep using the same formfactor file (automatically generated before the first BIG cycle). |
| ReuseGeometryFile [refine] overall refinement (BIG cycles) |
"yes" | From BIG cycle 2 onwards, keep using the same TNT restraints file (automatically generated before the first BIG cycle). |
| ReuseSequenceFile [refine] overall refinement (BIG cycles) |
"yes" | From BIG cycle 2 onwards, keep using the same TNT sequence file (automatically generated before the first BIG cycle or user-supplied). |
| RhoMacroMol [run_buster] refinement during each BIG cycle |
0.42 | Mean electron density of the macro-molecule. Standards are: 0.42 for a protein and 0.60 for a nucleic acid. |
| RhoSolvent [run_buster] refinement during each BIG cycle |
0.33 | Mean electron density of the solvent. |
| RmAnisou [refine] overall refinement (BIG cycles) |
"yes" | Should we remove ANISOU records from the input PDB file? |
| RmAnisouHydrogens [refine] overall refinement (BIG cycles) |
"yes" | Should we remove ANISOU records for hydrogens from the input PDB file? |
| RmLink [refine] overall refinement (BIG cycles) |
"no" | Should we remove LINK records from the input PDB file? |
| RmModres [refine] overall refinement (BIG cycles) |
"no" | Should we remove MODRES records from the input PDB file? |
| RunBusterPrintUsefulInfo [run_buster] refinement during each BIG cycle |
"no" | Should there be some additional (maybe useful) information/warnings given? |
| RunCor2Pdb [run_buster] refinement during each BIG cycle |
"yes" | Should we run "cor2pdb" when converting the ATOMC-formatted file after refinement into a PDB file? See also the UseGellyPdb parameter. |
| RunGellyNcsScreen [run_buster] refinement during each BIG cycle |
"no" | Should we create a ncs.lis file with the SCREEN output (showing outliers) for the current set of NCS restraints before starting the actual refinement in each BIG cycle?? |
| RunGellySanityCheck [run_buster] refinement during each BIG cycle |
"yes" | Should we run an initial sanity check (using Gelly) before starting the actual refinement in each BIG cycle? |
| RunGellyScreen [run_buster] refinement during each BIG cycle |
"yes" | Should we create a list of geometric values (and outliers) using Gelly before starting the actual refinement in each BIG cycle? |
| RunHarvest [run_buster] refinement during each BIG cycle |
"all" | Should we run the harvesting tool (for creating a fairly complete REMARK 3 header)? One of "no", "all" or "last". |
| RunPdb2Cor [run_buster] refinement during each BIG cycle |
"yes" | Should we run the "pdb2cor" tool when converting the initial PDB file into ATOMC format? |
| RunSfcheck [run_buster] refinement during each BIG cycle |
"yes" | Should we run SFCHECK (part of CCP4) to calculate the Luzatti coordinate error? |
| RunWilsonTwice [run_buster] refinement during each BIG cycle |
"no" | Do we need to run Wilson twice (to calculate even more exact solvent content)? |
| ScreenNumBuster [run_buster] refinement during each BIG cycle |
"100" | Maximum number of outliers to show for each restraint type (used internally in BUSTER for the screen_*.txt files) |
| ScreenSigmaBuster [run_buster] refinement during each BIG cycle |
"3.0" | All outliers above this value [sigma] for each restraint type will be shown in the screen_*.txt files. |
| ScreenSigmaInitial [run_buster] refinement during each BIG cycle |
"5.0" | All outliers above this value [sigma] for each restraint type will be shown in the initial geometry.lis file. |
| SequenceFileGeneration [ab_pdb2tnt] generation of TNT sequence file |
"MakeLINK" | Which tool to use for the generation of the TNT sequence file (one of "pdb2seq" or "MakeLINK"). |
| SetHydrogensBfixed [run_buster] refinement during each BIG cycle |
"yes" | Keep the isotropic B-factor parameters fixed for hydrogens. |
| SetNonHydrogensADP [run_buster] refinement during each BIG cycle |
"no" | Make all non-hydrogen atoms have individual anisotropic displacement parameters (ADP) unless there are already "NOTE BUSTER_ANISO_SET" cards specified. |
| SsbondSgDistanceMax [pdb2seq] generation of TNT sequence file |
"2.5" | When automatically detecting CYS:SG--CYS:SG bonds that aren't already specified: use this as longest allowed distance. |
| SsbondSgDistanceMin [pdb2seq] generation of TNT sequence file |
"1.5" | When automatically detecting CYS:SG--CYS:SG bonds that aren't already specified: use this as shortest allowed distance. |
| StandardDictionaries [various] standard dictionaries/databases |
"protgeo_eh99 exoticaa nuclgeo bcorrel contact idealdist_contact" | list of files (in $BDG_home/tnt/data) seen as the minimum set of standard dictionaries |
| StandardDictionariesAll [various] standard dictionaries/databases |
"protgeo_eh99 exoticaa nuclgeo sugar cofactor_geo othergeo bcorrel contact idealdist_contact assume connect" | list of files (in $BDG_home/tnt/data) seen as the complete set of standard dictionaries |
| StartFromPreviousWeightInPdb [refine] overall refinement (BIG cycles) |
"yes" | If the X-ray weight has been recorded in the REMARK 3 section of the input PDB file: should it be used as a starting value? |
| StopAfterBuster [refine] overall refinement (BIG cycles) |
"no" | Should we stop right after a BUSTER BIG cycle has finished? |
| StopAfterCmdServer [run_buster] refinement during each BIG cycle |
"no" | Should we stop right after the call to BUSTER has finished? |
| StopAfterGellySanityCheck [run_buster] refinement during each BIG cycle |
"no" | Should we stop right after the Gelly sanity check has been done? |
| StopAfterRunBuster [run_buster] refinement during each BIG cycle |
"no" | Should we stop right at the end of "run_buster"? |
| StopBeforeCmdServer [run_buster] refinement during each BIG cycle |
"no" | Should we stop right before the call to BUSTER? |
| StopOnCreatingEmptyLinkDictionary [pdb2seq] generation of TNT sequence file |
"no" | Should we stop when the creating of restraints (for two residues for which the connectivity is described on a LINK record in the PDB file) results in an empty dictionary? |
| StopOnDifferentSpacegroup [refine] overall refinement (BIG cycles) |
"yes" | Should we stop when the input PDB file and MTZ file have different spacegroups? |
| StopOnInitialXrayWeightFromPdbOutsideLimits [refine] overall refinement (BIG cycles) |
"yes" | Should we stop when the X-ray weight read from the PDB file header is outside the limits? |
| StopOnInitialXrayWeightOutsideLimits [refine] overall refinement (BIG cycles) |
"yes" | Should we stop when the X-ray weight given is outside the limits? |
| StopOnGellySanityCheckError [run_buster] refinement during each BIG cycle |
"yes" | Should we stop when the initial sanity check (by Gelly) reported some error? |
| StopOnMissingContactDistance [run_buster] refinement during each BIG cycle |
"no" | Should we stop when the initial check reports missing contact distances?? |
| TLSAutoFuseMultiCurly [refine] |
"yes" | detect and automatically fuse set specifications that have multiple curly-sets on a single BUSTER_TLS_SET record |
| TLSfixcycALL [refine] overall refinement (BIG cycles) |
"2" | from which BIG cycle onwards should all TLS parameters be fixed |
| TLSfixcycRB [refine] overall refinement (BIG cycles) |
"1" | from which BIG cycle onwards should the RB-part of TLS be fixed |
| TLSfreeze [refine] overall refinement (BIG cycles) |
"tls:B" | which atom selections should have their parameters frozen (i.e. keept constant) in the BIG cycles where TLS parameters are being refined. Specified by A:P, where A can be one of: all, tls, nottls, none, while P is a comma separated list of: XYZ, B, BIJ, OCC, ALL or NONE. E.g. to switch off the refinement of B and OCC for all atoms in TLS groups use TLSfreeze=tls:B,OCC |
| TlsUseFromPdbRemark3 [refine] overall refinement (BIG cycles) |
"yes" | If TLS refinement is switched on, but no TLSFile has been defined by user: should we try and extract the TLS sets (and optionally values) from the REMARK3 section of the input PDB file? |
| TntBfacMax [run_buster] refinement during each BIG cycle |
"300" | Upper limit for atomic temperature factors. |
| TntBfacMin [run_buster] refinement during each BIG cycle |
"3" | Lower limit for atomic temperature factors. |
| TntDictionary_assume [various] standard dictionary |
"$BDG_home/tnt/data/assume.dat" | file that enables easy handling of simple molecules (e.g. waters) |
| TntDictionary_bcorrel [various] standard dictionary |
"$BDG_home/tnt/data/bcorrel.dat" | standard dictionary with B-factor restraints for amino-acid residues |
| TntDictionary_cofactor [various] standard dictionary |
"$BDG_home/tnt/data/cofactor_geo.dat" | standard dictionary with restraints for common co-factors (ATP, FAD etc) |
| TntDictionary_connect [various] standard dictionary |
"$BDG_home/tnt/data/connect.dat" | file describing connectivity between standard residues (amino-acids, RNA/DNA, N- and C-terminal modifications, breaks, etc) |
| TntDictionary_contact [various] standard dictionary |
"$BDG_home/tnt/data/contact.dat" | database with minimum contact distances |
| TntDictionary_csdx [various] standard dictionary |
"$BDG_home/tnt/data/csdx_protgeo.dat" | old standard dictionary for amino-acids (Engh & Huber based) |
| TntDictionary_exoticaa [various] standard dictionary |
"$BDG_home/tnt/data/exoticaa.dat" | standard dictionary for exotic amino-acids (Engh & Huber 1999 based) |
| TntDictionary_formfactor [various] standard dictionary |
"$BDG_home/tnt/data/formfactor.dat" | database with form-factors for atoms (CuKa wavelength) |
| TntDictionary_idealdist [various] standard dictionary |
"$BDG_home/tnt/data/idealdist_contact.dat" | standard dictionary for ideal distances |
| TntDictionary_nuclgeo [various] standard dictionary |
"$BDG_home/tnt/data/nuclgeo.dat" | standard dictionary for nucleotides (RNA/DNA) |
| TntDictionary_othergeo [various] standard dictionary |
"$BDG_home/tnt/data/othergeo.dat" | standard dictionary for some other compounds (SO4, PO4, etc) |
| TntDictionary_pdbfixup [various] standard dictionary |
"$BDG_home/tnt/data/pdb_fixup.dat" | database to translate atom names from PDB file into atom types |
| TntDictionary_protgeo [various] standard dictionary |
"$BDG_home/tnt/data/protgeo_eh99.dat" | standard dictionary for amino-acids (Engh & Huber 1999 based) |
| TntDictionary_sugar [various] standard dictionary |
"$BDG_home/tnt/data/sugar.dat" | standard dictionary for sugars and sugar-linkages |
| TntWeightGeomRes [refine] overall refinement (BIG cycles) |
"no" | Should we get the updated X-ray weight through analysis of the geometric residual (default is to adjust X-ray weight based on rmsd(bond) value)? |
| TransferExoticAAFromSeqToGelly [refine] overall refinement (BIG cycles) |
"no" | Should we add any exotic amino-acid found during the initial generation of a TNT sequence file to the Gelly set definition named "ExoticAA"? |
| UpdateWaters [refine] overall refinement (BIG cycles) |
"no" | Should we update waters (same logic as the -noWAT/-WAT command-line switch)? |
| UpdateWatersEpdbOnly [refine] overall refinement (BIG cycles) |
"no" | Should the updated/new waters only be placed into the PDB file defining the bulk-solvent mask (and not the fragment part)? |
| UseBrefGroupFrom [refine] overall refinement (BIG cycles) |
"999.0" | Resolution limit below which only one B-factor per residue will be used. |
| UseBrefMcScFrom [refine] overall refinement (BIG cycles) |
"999.0" | Resolution limit below which two B-factors per residue will be used (one for main-chain and one for side-chain). |
| UseBrefNoneFrom [refine] overall refinement (BIG cycles) |
"3.5" | Resolution limit below which no B-factor refinement will be performed (only overall B-factor). |
| UseCcp4MonomerLibrary [pdb2tnt] |
"no" | provides fallback for unknown compounds |
| UseCrdScaleAfterCycle [refine] overall refinement (BIG cycles) |
"yes" | Should we use the refined scale factors after each BIG cycle for the next one? |
| UseCrdScaleAfterRigid [refine] overall refinement (BIG cycles) |
"no" | Should we use the refined scale factors after rigid body for the next BIG cycle? |
| UseDictionaryOrder [ab_pdb2tnt] generation of TNT restraints |
"msd ccp4 maketnt" | What is the preferred order for getting TNT restraint dictionaries for unknown residues? "msd" and "ccp4" will use restraints (if available) from $BDG_home/tnt/data/msd/ and $BDG_home/tnt/data/ccp4/, respectively. "maketnt" will create restraints based on the current coordinates of a given residue. |
| UseEpdbLastCycle [refine] overall refinement (BIG cycles) |
"yes" | Should the bulk-solvent mask in the last BIG cycle take into account any "excluded" regions (given e.g. by -x or -Lpdb flag - or defined automatically with the -L flag)? |
| UseGapAsBreakInSeq [pdb2seq] generation of TNT sequence file |
"no" | Instead of the default "BREAK" connection: should we use dummy "GAP" residues? |
| UseGellyPdb [run_buster] refinement during each BIG cycle |
"yes" | Should we use the final PDB file as written by Gelly after each BIG cycle? |
| UseHighResInRigid [refine] overall refinement (BIG cycles) |
"yes" | Should we use all reflections (up to high resolution limit) when doing an initial rigid-body refinement (if cell parameters have changed significantly)? |
| UseLinkFromGellyPdb [run_buster] refinement during each BIG cycle |
"yes" | Should we use LINK records from the final PDB file (at the end of each BIG cycle) coming from Gelly? |
| UseLlgradAsFoFc [refine] overall refinement (BIG cycles) |
"no" | Instead of using "normal" Fo-Fc difference maps: should we use LLG-maps instead? |
| UseLlzThroughout [refine] overall refinement (BIG cycles) |
"no" | Should we keep the initial zero-level log-likelihood values for all BIG cycles (to calculate log-likelihood gain relative to the initial values and not relative to the starting values at each BIG cycle)? |
| UseLowResInRigid [refine] overall refinement (BIG cycles) |
"yes" | Should we use all low-resolution data when doing rigid-body refinement (or cut it at 6 Å)? |
| UseLpdbLastCycle [refine] overall refinement (BIG cycles) |
"yes" | Should the bulk-solvent mask in the final BIG cycle take the PDB file given with the -Lpdb flag into account? |
| UseMakeTntAuto [dic2tnt] converting restraint dictionaries on the fly |
"no" | Should all user-supplied dictionaries be passed through "MakeTNT -auto"? |
| UseMapAsNup [refine] overall refinement (BIG cycles) |
"no" | Should we use a map (from current phases) as source for non-uniform prior? |
| UseMapAsSlv [refine] overall refinement (BIG cycles) |
"no" | Should we use a map (from current phases) as source for bulk-solvent mask? |
| UseMaxEntLastCycle [refine] overall refinement (BIG cycles) |
"no" | Should we run a maximum-entropy completion at the last BIG cycle? |
| UseMaxEntThroughout [refine] overall refinement (BIG cycles) |
"no" | Should we run a maximum-entropy completion at every BIG cycle? |
| UseMtzchk [refine] overall refinement (BIG cycles) |
"yes" | Should we use the "mtzchk" tool for analysing and checking the input MTZ file? |
| UseMxlcycLastCycle [refine] overall refinement (BIG cycles) |
"yes" | Should we run refinement cycles (small cycles) at the last BIG cycle? |
| UseNmissLastCycle [refine] overall refinement (BIG cycles) |
"no" | Should we use the missing part at the last BIG cycle? |
| UseNmissThroughout [refine] overall refinement (BIG cycles) |
"no" | Should we use the missing part at every BIG cycle? |
| UsePdbchk [refine] overall refinement (BIG cycles) |
"yes" | Should we use the "pdbchk" tool for analysing and checking the input PDB file? |
| UsePdbcmb [run_buster] refinement during each BIG cycle |
"yes" | Should we use the "pdbcmb" tool to combine existing header records with updated information (from harvesting)? |
| UseRefmacdict2tnt [dic2tnt] converting restraint dictionaries on the fly |
"yes" | Should we use the "refmacdict2tnt" tool to automatically convert CCP4/REFMAC dictionaries (*.cif) into TNT format? |
| UseSortwater [maptools] various steps involving maps |
"no" | Should we use the CCP4 program "sortwater" to move updated water molecules closer to PDB file? |
| WaterChainId [various] water updating |
"W" | Use this chain identifier for waters on output if possible (column 22 on ATOM/HETATM records of PDB files) |
| WaterFindSigma [maptools] various steps involving maps |
"3.2" | Cut-off level [rms] for difference (Fo-Fc) map to find new water molecules in. |
| WaterFindSigmaLlg [maptools] various steps involving maps |
"6.0" | Cut-off level [rms] for log-likelihood gradient map to find new water molecules in. |
| WaterMinDistance [maptools] various steps involving maps |
"2.5" | Minimum distance newly added waters should have to already existing atoms. |
| WaterNamingAtom [various] water updating |
" O " | atom name of water molecules on output (column 13-16 on ATOM/HETATM records of PDB files) |
| WaterNamingResidue [various] water updating |
"HOH" | residue name of water molecules on output (column 18-20 on ATOM/HETATM records of PDB files) |
| WaterPickingOptimise [maptools] various steps involving maps |
"no" | When picking peaks (using PKMAPS): should the initial peak positions be optimized? |
| WaterPickingHydrogenPartner [maptools] various steps involving maps |
"no" | When picking peaks (using PKMAPS): do we require those peaks to be within distance of a hydrogen bonding partner? |
| WaterPickingHydrogenPartnerAll [maptools] various steps involving maps |
"no" | Do we accept all residue types as potential hydrogen bonding partners (or only protein residues)? |
| WaterRemoveDeleted [maptools] various steps involving maps |
"0.5" | Any waters closer than this distance [Å] to previously deleted waters will not be added (again). |
| WaterRemoveDistFac [maptools] various steps involving maps |
"0.16666" | Used in conjunction with high resolution limit to define a maximum distance an existing water atom is allowed to be away from a peak in the 2Fo-Fc map (otherwise it will be removed). |
| WaterRemoveHpartner [maptools] various steps involving maps |
"3.5" | If a hydrogen bonding partner is required: upper limit distance criteria. |
| WaterRemoveMerge [maptools] various steps involving maps |
"2.2" | Water molecules closer than this distance [Å] will be merged into a single water atom (when using ARP_WATERS). |
| WaterRemoveSigma [maptools] various steps involving maps |
"0.8" | Water molecules with density less than this value [rms] in the 2Fo-Fc map will be removed. |
| WaterResidueNames [various] user-supplied PDB file |
"HOH WAT" | list of residue names that are recognized as being water/solvent in user-supplied PDB file |
| WaterUpdateFftResMin [maptools] various steps involving maps |
"1.5" | Minimum high resolution limit for calculating maps (during water updating). |
| WaterUpdateProgram [refine] overall refinement (BIG cycles) |
"PKMAPS" | Program to use for updating (addition/deletion) of water molecules (can be one of "PKMAPS", "ARP_WATERS" or the absolute path to a user-supplied program/script). For an example of a user-supplied script: check the water_updater.sh template as an example! |
| XrayWeight_max [refine] overall refinement (BIG cycles) |
"50.0" | Maximum value of X-ray weight that can be reached during automatic adjustment. |
| XrayWeight_min [refine] overall refinement (BIG cycles) |
"1.0" | Minimum value of X-ray weight that can be reached during automatic adjustment. |
| XrayWeight_start [refine] overall refinement (BIG cycles) |
"4.0" | Starting value of X-ray weight (which might be adjusted
automatically (see also -r and parameter KeepCurrentRmsBond) Note: the unit of X-ray weights has changed (by a factor of 1/100) as of 07/2009 - instead of an integer value (typically in the range 400-5000) the real weight (typically between 4.0 and 50.0) should be given. |
| autoBUSTER_ShiftOutputModelBack [refine] |
"yes" | if the input model got corrected by pdbchk (shifting closer to origin): should we shift it back to the original/input position? |
| autoBUSTER_MacroDirs [general] |
"" | colon-separated list of directories with additional (user-supplied) *.macro files |
| autoBUSTER__FsigF_Pairs [refine] overall refinement (BIG cycles) |
"" | List of (space-separated) F,SIGF pairs in the MTZ file to be refined against e.g. "FP,SIGFP Fnat,SIGFnat". Default is all pairs of column type "F" followed by column type "Q". |
| autoBUSTER_hls [refine] overall refinement (BIG cycles) |
"no" | List of (space-separated) Hendrickson-Lattman coefficients in the MTZ file to be refined against e.g. "HLA HLB HLC HLD". Specify "no" to switch off and "" for the automatic usage unless from BUSTER. Default is to not use them. |
| blkblr [run_buster] refinement during each BIG cycle |
"50" | Bulk-solvent mask blurring B-factor [Å2]. |
| blkrad [run_buster] refinement during each BIG cycle |
"215" | Bulk-solvent mask radius [1/100th Å]. |
| do_analyse [refine] presentation of results |
"yes" | Should we run final analysing step (creates analyse.html file)? |
| do_maps [refine] presentation of results |
"yes" | Should we create final maps (Fo-Fc and 2Fo-Fc)? |
| frgrad [run_buster] refinement during each BIG cycle |
"215" | Fragment mask radius [1/100th Å]. |
| mskblr [run_buster] refinement during each BIG cycle |
"50" | Non-uniform prior (NUP) mask blurring B-factor [Å2]. |
| mskisl [run_buster] refinement during each BIG cycle |
"0" | Should we try and remove islands during masking in BUSTER? |
| mskrad [run_buster] refinement during each BIG cycle |
"400" | Non-uniform prior (NUP) mask radius [1/100th Å]. |
| mxlcyc_start [refine] overall refinement (BIG cycles) |
"100" | Starting value for number of small cycles. |
| nmiss [refine] overall refinement (BIG cycles) |
"0" | Number of atoms that are unmodelled so far. |
| nthreads [run_buster] refinement during each BIG cycle |
fraction of available | How many threads should be used for running BUSTER: can be modified through the "-nthreads" command-line argument to "refine". See Controlling the number of threads for details. |
| refmacdict2tnt_args [dic2tnt] converting restraint dictionaries on the fly |
"" | extra arguments for refmacdict2tnt tool |
| refocc [run_buster] refinement during each BIG cycle |
"off" | Should we refine occupancies? |
| refscl_rfr [run_buster] refinement during each BIG cycle |
"0" | Should we refine scale factor of missing part? |
| refscl_rfs [run_buster] refinement during each BIG cycle |
"1" | Should we refine scale factor of bulk solvent? |
| refscl_rif [run_buster] refinement during each BIG cycle |
"1" | Should we refine imperfection B-factor for fragment? |
| refscl_rir [run_buster] refinement during each BIG cycle |
"0" | Should we refine imperfection B-factor for missing part? |
| refscl_ris [run_buster] refinement during each BIG cycle |
"1" | Should we refine imperfection B-factor for bulk solvent? |
| refscl_rkim [run_buster] refinement during each BIG cycle |
"0" | Should we refine imperfection scale factor for missing part? |
| refscl_rkis [run_buster] refinement during each BIG cycle |
"0" | Should we refine imperfection scale factor for bulk solvent? |
| rmsBOND_target [refine] overall refinement (BIG cycles) |
"0.010" | Target value rms(bond) for adjusting X-ray weight automatically. |
| solc [run_buster] refinement during each BIG cycle |
"" | solvent content [fraction]; default is to determine this automatically based on current PDB file |
| wavelength [run_buster] refinement during each BIG cycle |
"1.54180" | Wavelength of reflection data. |