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Additional tools |
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 authorised
only pursuant to a valid written licence from GPhL.
Contact
buster-develop@GlobalPhasing.com
This is a utility that will check programs in the BUSTER suite in turn. checkdeps makes sure that all the required 3rd party tools are installed, available and function properly. Problems are indicated on lines starting "ERROR". If no problems are found then this is shown by "SUCCESS". The utility prints out a summary of results found at the end. The script's exit status will be 0 for success but 1 if any problem is found
currently checkdeps runs:
For help in configuring the software including advice on how to use checkdeps see the detailed installation instructions..
checkdeps command line option:
Parameter | Options | Explanation | Remark |
---|---|---|---|
-n | turn off the prompt for user to hit the Enter key before running each check |
% corr -p refine.pdb -m refine.mtz -F 2FOFCWT -P PH2FOFCWT |
which will produce overall and per-residue correlation coefficients on standard output as well as some PLOTMTV-formatted files of main-chain and side-chain correlation plots (e.g. named refine_CC-mc_Chain-A.mtv).
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-p | <PDB file> | PDB file with standard CRYST1 card | |
-m | <MTZ|MAP file> | MTZ or MAP file | MTZ file with columns for F, PHI and (optionally) WEIGHT or MAP file in CCP4 format |
-F | <F> | amplitude | |
-P | <PHI> | phase | |
-Fc | <Fcalc> | (optional) amplitude of model | default is to calculate structure factors of model from input PDB file (which will then not contain bulk-solvent correction or anisotropic scaling) |
-Pc | <PHIcalc> | phase of model | |
-a | <atom name> | rename atoms to this name | done before the CC calculation |
-d | <subdir> | directory name | results are expected in this sub-directory and all files will be created there too |
-R | <resl> <resh> | low- and high-resolution limits | MTZ file: default is to use full resolution range from this file |
-W | <WEIGHT> | (optional) weight | usual coefficients (2FOFCWT, PH2FOFCWT) are already correct map coefficients, so this doesn't need to be given |
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-f | force overwriting of files | default= stop if a file would be overwritten | |
-p | <PDB file> | PDB file to be refined | |
-o | <output file> | output PDB file | |
-d | <subdir> | all (temporary) o/p will be written to directory | default = current directory |
-l | <dictionary> | additional restraints dictionary files | several -l flags can be given; default is to use the standard dictionaries distributed BUSTER |
-s | <space-group> | space-group name | default = pick from CRYST1 card of PDB file |
-c | <cell parameters> | cell parameters a, b, c, alpha, beta, gamma | default = pick from CRYST1 card of PDB file |
-Seq | <TNT sequence file> | TNT sequence file | default = create on-the-fly from input PDB file |
-I | <Identifier> | automatically generated files will start with the string <Identifier> | default = "gelly" |
-jiggle_xyz | <rms> | adds a random perturbation (jiggle) to all input atoms before starting refinement | The size of this perturbation is given as a mean rms deviation (default is to not jiggle) |
Any command-line options not in the above list will be passed directly to the gelly binary; see GELLY for a list of useful options, and a couple of usage examples.
Additionally, the following parameters are defined (which can be overwritten on the command line, using the parameter=value syntax):
Parameter | Default | Explanation | Remark |
---|---|---|---|
weight_bond | 2.0 | bond distances | |
weight_angle | 2.0 | bond angles | |
weight_improper | 0.0 | improper angles | |
2.0 | if all residues in input PDB file are described by user-supplied dictionary files (via the -l flag) | ||
weight_torsion | 0.0 | torsion angles | |
2.0 | if all residues in input PDB file are described by user-supplied dictionary files (via the -l flag) | ||
weight_pseudo | 0.0 | ||
2.0 | if all residues in input PDB file are described by user-supplied dictionary files (via the -l flag) | ||
weight_trigonal | 2.0 | ||
weight_plane | 5.0 | planarity | |
weight_contact | 5.0 | contact distances | |
weight_bcorrel | 0.0 | B-factor correlation of bonded atoms | |
weight_chiral | 5.0 | chirality |
Parameter | Options | Explanation | Remark |
---|---|---|---|
-h | Print brief help message | ||
-man | Print man page for full description |
Parameter | Options | Explanation | Remark |
---|---|---|---|
-h | Print brief help message | ||
-man | Print man page for full description |
Parameter | Options | Explanation | Remark |
---|---|---|---|
-h | Print brief help message | ||
-man | Print man page for full description |
This is a tool for adding hydrogen atoms to proteins and/or ligands; it requires the 'reduce' program (distributed as part of CCP4 or the MolProbity suite) to be on the PATH or to be defined using the $BDG_TOOL_MOLPROBITY_ROOT environment variable.
It might be easiest to run "aB_hydrogenate" (which is a
wrapper around "hydrogenate"), since this will (1)
automatically add missing compound dictionaries (from the CCP4 monomer
library) to ensure all residues are hydrogenated and (2) perform
various fixes on the initial result (there are some limitations in
'reduce' when it comes to alternate conformations and/or terminal
residues).
Parameter for hydrogenate | Options | Explanation | Remark |
---|---|---|---|
-checkdeps | Check that all the dependencies are present | Special option that checks that the external tools required (reduce) have been setup properly. This option is one of the tests run by the checkdeps script. | |
-p | <input filename> | Protein to hydrogenate | |
-o | <output filename> | Name for the output file | |
-l | <dictionary1.cif> <dictionary2.cif> ... | List of CIF-format dictionaries for the ligands | hydrogenate writes out a list of the residue IDs it was unable to hydrogenate; you will want to provide dictionaries for most of them (though obviously not metals); grade_PDB_ligand will be helpful for this. |
-ligonly | Only hydrogenate the ligands | ||
-full | Add hydrogens with full occupancy (i.e. the same as the carrying atom) instead of zero occupancy | ||
-f | Overwrite the output if it already exists | ||
-ecloud | place hydrogens at electron-cloud (instead of nuclear) position |
% mk_coot_macros.sh |
% coot --script Coot.scr |
% mk_pymol_macros.sh |
% pymol pymol.pml |
Please note that you can't use standard output (captured in a file) directly as a TNT sequence file. If you want to create a file please use the -o command line argument.
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-p | <PDB file> | PDB file following the recommendations | |
-o | <output file> | (optional) output file for TNT sequence | default is standard output |
By default chain breaks in the input PDB file will be converted into BREAK statements in the resulting sequence file. If the parameter UseGapAsBreakInSeq is set to yes (on the command line: UseGapAsBreakInSeq=yes), then a so-called GAP-residue is used instead. The effect is that a range-definition (e.g. for defining a rigid-body) can 'step over' a GAP-residue but not over a BREAK.
This tool can be used to make sure a PDB file conforms to most of the PDB format standards as well as some slightly more stringent requirements for BUSTER and BUSTER.
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-p | input file | PDB formatted coordinate file | |
-o | output file | (optional) PDB formatted coordinate file | the presence of this optional argument triggers functionality within "pdbchk" that will try and fix any encountered problems of the input file |
The list of tests performed (in this order) is:
Test (name) | Explanation | Fixing |
---|---|---|
NoCryst1 | checking if we're missing CRYST1 record | - |
Cell | checking for cell parameters on CRYST1 record | - |
NoSpacegroup | checking if CRYST1 doesn't contain a spacegroup | - |
Spgr | checking for spacegroup name on CRYST1 record | - |
EmptyLines | checking for empty records | - |
HaveCoordinateRecords | checking if we have any coordinate records | - |
RecordsStartingWithSpace | checking if we have any records starting with a space | - |
SeveralModels | checking if PDB file contains several models | - |
WeirdCellParameters | checking if cell parameters on CRYST1 are weird | - |
WeirdCellVolume | checking if cell volume (from CRYST1 record) is weird | - |
BarSpacegroup | checking if spacegroup symbols has 'bar' (e.g. P -1/P 1-) | change spacegroup symbol (e.g. from "P 1-" to "P -1" |
R3H3 | checking if R3/R32/R3m/R3c is meant to be H3/H32/H3m/H3c | change spacegroup symbol (e.g. from "R 3" to "H 3" |
UnknownSpacegroup | checking if spacegroup name is unknown | - |
CellSpacegroupInconsistency | check if cell and spacegroup are consistent | - |
UnknownTntSpacegroup | checking if for given spacegroup we have a TNT equivalent | - |
RecordsStandardOrder | checking if records are in standard order | records will be reordered according to PDB Format (up to CRYST1 record) |
RecordFormat | checking if some crucial records have correct format | - |
SsbondIsCys | checking if SSBOND records contain only CYS residues | - |
ResidueNumbersOnRecordsAreInteger | check if residue numbers on records are Integer | re-write residue numbers as integers on records SEQADV, MODRES, HET, SSBOND, CISPEP, LINK, SLTBRG, HYDBND, SITE, ATOM and HETATM |
ResidueNumberInsertionCodeFive | checking if residue number > 999 and insertion code present (TNT limitation) | - |
EmptyAtomNameOnLinkRecord | check if LINK records contain empty atom names (in both positions) | remove those LINK records |
WrongReferenceToCoordinateRecord | checking for wrong references to coordinate records | - |
NoChainId | checking for ATOM/HETATM records without chain identifier | add new chain ID to records without one (this includes the following records: DBREF, SEQADV, SEQRES, MODRES, HET, SSBOND, LINK, HYDBND, SLTBRG, CISPEP, SITE, ATOM, SIGATM, ANISOU, SIGUIJ, TER and HETATM) |
OxyResidueName | checking if there are residues called "OXY" (special treatment in TNT) | residues will be renamed from "OXY" to " O2" (if the "OXY" residue contains atoms " O1 " and " O2 ") |
DuplicateChainRes | checking for ATOM/HETATM records where the same chainID+resSeq+iCode is used for different resName | if possible, adding chain ID "W" to water residues (residue name "HOH") |
StandardResiduesHetatm | checking if standard residues have (wrong) HETATM record | change record from HETATM to ATOM |
NonStandardResiduesAtom | checking if non-standard residues have (wrong) ATOM record | change record from ATOM to HETATM |
BfactorNegative | checking if ATOM/HETATM records have negative B-factors | set B-factor to zero |
OccRange | checking if ATOM/HETATM records have occupancy in range 0.0 ... 1.0 | limit occupancy to range zero to one |
AlternateConformationsOccSum | checking if alternate conformations of ATOM/HETATM records have an occupancy sum in range 0.0 ... 1.0 | - |
AtomNamesWithSpaces | checking if atom names have space in them | replaces spaces by underscore "_" |
ElementType | checking if element type is present and consistent with atom name | guesstimate element from atom name |
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-s | ASCII sequence file | file with (upper-case) protein sequence | |
-i | ResNumStart | starting residue number | default = 1 |
-c | ChainId | 1-character chain identifier | default = " " |
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-p | PDB file |
Consecutive residues with alternate conformations and same occupancy will be grouped together. If only two alternate conformations are given for a residue, then their summed occupancy will be restrained to 1.0.
If specific residues are given with the -r flag, only those will be considered irrespective of their occupancy value.
For further details on how to use pdb2occ and how to perform occupancy refinement see the occupancy refinement tutorials on the BUSTER wiki.
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-p | PDB file | input PDB file | |
-o | output file | optional | output file containing Gelly-syntax |
-r | res | optional | residue specification given as residue name (e.g. "ADP") or residue number including chain identifier (e.g. "A|207"); multiple -r flags can be given |
Flag | Arguments | Explanation | Remark |
---|---|---|---|
-p | PDB file | ||
-o | output TLS file | optional | |
-a | autotype | use automatic definition for BUSTER. The automatic definition type can be one of "EachMacroMolChain" or "OnePerChain". Default is "EachMacroMolChain". |
The typical usage would be:
% refmacdict2tnt <restraint file> <TNT output file> [<PDB output file] |
Note that BUSTER can usually handle cif restraint dictionaries directly if you pass them using the -l flag; if you find yourself routinely converting them manually, please contact buster-develop@globalphasing.com and we will try to make your work-flow easier.
Note that the flags for refmacdict2tnt must go before the filenames
Flag | Explanation | Remark |
---|---|---|
-nopdb | Don't extract atom-position information from the input .cif file | If you don't use this option, you need to specify a filename for the PDB output |
-believetorsions | Preserve sigma values when translating torsion cards in the input | |
-notorsions | Ignore all torsion cards in the input | |
-oneplane | Do not output an extra, dehydrogenated version of any plane containing hydrogens | If any atom in a plane is missing then BUSTER will not apply that plane restraint at all - so if your input dictionary has large planes containing hydrogens, and you are refining a model lacking hydrogens, you must use -oneplane |
-fixplanesigma | Tweak sigma values for planes so that the TNT and CCP4/REFMAC geometry functions give identical values | |
-tlc XXX | Set three-letter code to use for the single ligand in the CIF file | |
-model abc.pdb | Convert only ligands which appear in abc.pdb with a HETSYN card containing a synonym of the form +id; use the three-letter code that appears in that HETSYN card. | This option (introduced in early 2012) is intended to make it easier to work with compound libraries without having to worry about unique three-letter codes for each ligand |
For help on its use see BUSTER Output Interpretation page on the BUSTER wiki.
The procedure is run
% visualise-geometry-coot <BUSTER refinement directory> |
% diff_fourier -h |
Upon successful running, the script will create several output files -
the prefix of which can be set with the -o
flag. Other
potentially useful flags (for full details see output of
-h
):
-keepmap
: to keep the calculated map file (CCP4 format, which can be loaded into Coot directly)-R <resl> <resh>
: to set resolution limits (eg. restricting to only data with anomalous signal)-negative
: to also look for negative peaks (but then the -pdb
option has no effect)% diff_fourier -m truncate.mtz -p refine.mtz -P PH2FOFCWT FOM -o AnoFourier |
truncate.mtz
(default: first D/Q column pair - e.g. DANO/SIGDANO)PH2FOFCWT
and weight FOM
from file refine.mtz
If a PDB file (consistent with the phases) is also given with
% diff_fourier -m truncate.mtz -p refine.mtz -P PH2FOFCWT FOM -o AnoFourier -pdb refine.pdb |
============================================================================ mtz ......................................... truncate.mtz F ........................................... F SIGF ........................................ SIGF DANO ........................................ DANO SANO ........................................ SIGDANO pmtz ........................................ refine.mtz PHI ......................................... PH2FOFCWT FOM ......................................... FOM pdb ......................................... refine.pdb ... 7 peaks above 20 sigma 9 peaks above 15 sigma 11 peaks above 10 sigma 11 peaks above 8 sigma 12 peaks above 6 sigma 12 peaks above 5 sigma 37 peaks above 4 sigma -rw-r--r-- 1 vonrhein vonrhein 2132 Oct 10 15:29 AnoFourier.ANO.compare -rw-r--r-- 1 vonrhein vonrhein 13940 Oct 10 15:29 AnoFourier.ANO.hatom -rw-r--r-- 1 vonrhein vonrhein 24715 Oct 10 15:29 AnoFourier.ANO.pdb
AnoFourier.ANO.compare:
Peak Closest atom in refine.pdb [rms] Distance (<= 1.0 ) ------------------------------------------------------------------------- 31.23 <=> SE MSE F 7 ( 0.84 40.87) : 0.07 30.91 <=> SE MSE A 7 ( 0.84 45.76) : 0.04 30.22 <=> SE MSE A 126 ( 0.66 45.08) : 0.08 29.08 <=> SE MSE F 126 ( 0.66 40.55) : 0.13 23.72 <=> SE MSE F 137 ( 0.73 42.17) : 0.06 22.10 <=> SE MSE A 137 ( 0.73 45.81) : 0.13 21.10 <=> SE MSE F 293 ( 0.88 70.46) : 0.27 18.64 <=> SE MSE F 139 ( 0.58 47.16) : 0.32 16.20 <=> SE MSE A 293 ( 0.88 93.55) : 0.43 14.81 <=> SE MSE A 139 ( 0.58 53.66) : 0.26 11.24 <=> SE MSE F 1 ( 0.56 72.94) : 0.19 7.26 <=> SE MSE A 1 ( 0.56 92.71) : 0.49 4.10 <=> O THR A 161 ( 1.00 43.14) : 0.92 3.81 <=> CB THR F 261 ( 1.00 65.06) : 0.58 ...
AnoFourier.ANO.hatom:
ATOM Se -0.0623 -0.0435 0.3244 31.23 ATOM Se 0.0630 -0.0264 -0.2195 30.91 ATOM Se -0.0761 0.0141 -0.0840 30.22 ATOM Se 0.0776 0.0031 0.1880 29.08 ATOM Se -0.0028 -0.1375 0.2705 23.72 ATOM Se 0.0042 -0.1241 -0.1671 22.10 ATOM Se -0.0712 0.2201 0.1354 21.10 ATOM Se -0.0261 -0.1020 0.3066 18.64 ATOM Se 0.0787 0.2230 -0.0277 16.20 ATOM Se 0.0204 -0.0827 -0.2023 14.81 ATOM Se -0.3329 -0.1845 0.3639 11.24 ATOM Se 0.3373 -0.1699 -0.2602 7.26 ATOM Se 0.0752 -0.1320 0.2399 4.56 ...
AnoFourier.ANO.pdb:
CRYST1 62.827 90.075 191.529 90.00 90.00 90.00 P 21 21 21 SCALE1 0.015917 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011102 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005221 0.00000 ATOM 182 C DUM 1 -3.916 -3.917 62.136 1.00 31.23 11 ATOM 136 C DUM 2 3.955 -2.381 -42.043 1.00 30.91 11 ATOM 313 C DUM 3 -4.783 1.274 -16.088 1.00 30.22 11 ATOM 24 C DUM 4 4.875 0.282 36.013 1.00 29.08 11 ATOM 172 C DUM 5 -0.178 -12.385 51.807 1.00 23.72 11 ATOM 170 C DUM 6 0.264 -11.178 -32.014 1.00 22.10 11 ATOM 319 C DUM 7 -4.476 19.827 25.928 1.00 21.10 11 ATOM 173 C DUM 8 -1.639 -9.191 58.728 1.00 18.64 11 ATOM 33 C DUM 9 4.943 20.085 -5.303 1.00 16.20 11 ATOM 154 C DUM 10 1.282 -7.447 -38.744 1.00 14.81 11 ATOM 281 C DUM 11 -20.916 -16.621 69.699 1.00 11.24 11 ATOM 62 C DUM 12 21.190 -15.308 -49.836 1.00 7.26 11 ATOM 133 C DUM 13 4.726 -11.886 45.946 1.00 4.56 11 ...
So we have
% diff_fourier -m apo.mtz -p apo_refine.mtz -P PH2FOFCWT FOM -m2 inhibitor.mtz -o IsoFourier -pdb apo_refine.pdb -noANO -compare_cut 10.0 |
apo.mtz
inhibitor.mtz
apo_refine.mtz
)F_inhibitor-F_apo
map============================================================================ mtz ......................................... apo.mtz F ........................................... FP SIGF ........................................ SIGFP DANO ........................................ SANO ........................................ pmtz ........................................ apo_refine.mtz PHI ......................................... PH2FOFCWT FOM ......................................... FOM pdb ......................................... apo_refine.pdb mtz2......................................... inhibitor.mtz F2 .......................................... FP SIGF2 ....................................... SIGFP ... 0 peaks above 20 sigma 0 peaks above 15 sigma 0 peaks above 10 sigma 2 peaks above 8 sigma 3 peaks above 6 sigma 5 peaks above 5 sigma 20 peaks above 4 sigma -rw-r--r-- 1 vonrhein vonrhein 1846 Oct 10 15:56 IsoFourier.ISO.compare -rw-r--r-- 1 vonrhein vonrhein 6068 Oct 10 15:56 IsoFourier.ISO.hatom -rw-r--r-- 1 vonrhein vonrhein 10891 Oct 10 15:56 IsoFourier.ISO.pdb
This will show positive peaks where data in inhibitor.mtz
predicts density that is absent in apo.mtz
, eg. for an
inhibitor:
IsoFourier.ISO.compare:
Peak Closest atom in apo_refine.pdb [rms] Distance (<= 10.0 ) ------------------------------------------------------------------------- 9.37 <=> O HOH A 501 ( 1.00 27.89) : 1.97 8.72 <=> NZ LYS A 89 ( 1.00 43.51) : 0.87 6.85 <=> O HOH A 505 ( 1.00 44.68) : 2.09 5.99 <=> O HOH A 505 ( 1.00 44.68) : 1.68 5.48 <=> O HOH A 508 ( 1.00 41.07) : 2.34 4.85 <=> CB LYS A 89 ( 1.00 30.25) : 2.54 4.47 <=> CG2 ILE A 186 ( 1.00 12.12) : 1.45 ...
If we had already a model of the inhibitor and used that PDB file instead:
% diff_fourier -m apo.mtz -p apo_refine.mtz -P PH2FOFCWT FOM -m2 inhibitor.mtz -o IsoFourier -pdb inhibitor.pdb -noANO |
Peak Closest atom in inhibitor.pdb [rms] Distance (<= 1.0 ) ------------------------------------------------------------------------- 9.37 <=> C10 DT4 A1299 ( 1.00 38.54) : 0.32 8.72 <=> S1 DT4 A1299 ( 1.00 54.82) : 0.31 6.85 <=> N5 DT4 A1299 ( 1.00 43.09) : 0.54 5.99 <=> C15 DT4 A1299 ( 1.00 47.69) : 0.81 5.48 <=> N7 DT4 A1299 ( 1.00 43.13) : 0.68 4.85 <=> CD LYS A 89 ( 1.00 43.87) : 0.56 4.32 <=> NZ LYS A 33 ( 1.00 41.01) : 0.68 4.26 <=> C PRO A 171 ( 1.00 30.06) : 0.84 4.02 <=> C4 DT4 A1299 ( 0.75 45.81) : 0.85 ...showing us the peaks being very close to the inhibitor.
The output could be useful to get a quick and automatic idea about the amount of difference density features around specific residues (like co-factors, active-site residues or ligands).
A typical usage could be (see also help messages with the "-h" flag):
% ana_diffmap_residue -p refine.pdb -m refine.mtz |
A large number of additional checks and analysis are carried out - eg to inform the user about inconsistencies between
If a local copy of the PDB archive is available, the environmental variable BDG_TOOL_LOCALPDBDIR can be set to the full path of this directory (it expects to then find $BDG_TOOL_LOCALPDBDIR/data/structures/all/).
The typical usage for PDB identifier "1ABC" would be:
% fetch_PDB 1ABC |
We are using bond distance (between the two Cys-SG atoms), angle (between Cys1-CB, Cys1-SG and Cys2-SG) and torsion angle (Cys1-CB, Cys1-SG, Cys2-SG and Cys2-CB) as criteria. Based on some data harvesting of deposited PDB structures (refined with BUSTER or REFMAC - since Phenix-refined structures have a different torsion angle distribution with distinct "spikes") we have
|
The generation of the remaining files is automated via the aB_covalent_ligand tool:
% aB_covalent_ligand <PDB file> |
Example 1:
We look at 4ZZO as an example - starting as if we only had (a) the APO structure, (b) a dataset of the ligand-bound form and (c) the SMILES string for the bound ligand. The required files can be generated via the following commands:
% fetch_PDB 4ZZO | tee 4ZZO.lis % grep -v "CQ3" 4ZZO/4zzo.pdb > apo.pdb % ln -s 4ZZO/4zzo-unique.mtz compound.mtz |
We now want to refine the "APO" structure against the compound dataset, e.g. using:
% refine -p apo.pdb -m compound.mtz -RB -d buster.01 | tee buster.01.lis |
Now we can generate a CIF dictionary for the compound and fit it into the difference density of the above refinement:
% grade 'CCC(=O)Nc1ccccc1Nc1nc(NC2CCOCC2)ncc1Cl' -resname CQ3 | tee grade_CQ3.lis % rhofit -l grade-CQ3.cif -m buster.01/refine.mtz -p buster.01/refine.pdb -d rhofit | tee rhofit.lis |
If there is no access to a local installation of the Cambridge Structural Database (CSD), the dictionary can also be generated on the Grade Web Server.
The results from the Rhofit run can be visualised by:
% cd rhofit % visualise-rhofit-coot |
Here one can
LINK C CQ3 A4000 SG CYS A 166 1555 1555 |
% cd rhofit % coot --pdb merged.pdb --auto refine.mtz --dictionary best.cif |
and work on the already combined model (top hit and APO part).
Everything up to this part is just preparation to have the correct PDB file as described above: ligand fitted in appropriate pose and correct LINK record. There is no reason why this couldn't be done any other way: other than the final PDB file, nothing else is required for the actual step of creating a linkage restraints dictionary and the auxilliary files for refinement in BUSTER.
We can now run:
% aB_covalent_ligand merged_link.pdb | tee aB_covalent_ligand.lis |
which will report at the end:
For MakeLINK = CQ3-C_CYS-SG.dat For BUSTER = CQ3-C_CYS-SG.dic Run with e.g. refine -p merged_link.pdb \ -m some.mtz \ -l grade-LIG.cif \ MakeLINK_LinkagesFile=CQ3-C_CYS-SG.dat \ -l CQ3-C_CYS-SG.dic \ RunBusterDuplicatesOverride=CQC \ ... - or - refine -p merged_link.pdb \ -m some.mtz \ -l grade-LIG.cif \ -M /some/where/rhofit/CQ3-C_CYS-SG.macro \ ... |
This means we can now run a BUSTER refinement of the covalently bound ligand using:
% refine -p rhofit/merged_link.pdb -m compound.mtz \ -l grade-CQ3.cif -M /some/where/rhofit/CQ3-C_CYS-SG.macro \ -d buster.02 | tee buster.02.lis |
(of course adapting the actual command-line according to the model parametrisation - like NCS, TLS, occupancy refinement, additional restraints etc). In this particular example, the R/Rfree values go from 0.1966/0.2524 (initial APO refinement) to 0.1869/0.2411 after final refinement of the protein-ligand complex with the ligand covalently bound.