- modeller_usage - salilab.org

Building multi-chain models
by alina.s123567＠gmail.com 06 Jun '24

06 Jun '24

Good day, I would like to build a GABA A receptor with (two alpha2 subunits chain A, D), (two beta2 subunits chain B, E) and (one gamma subunit chain C). I create an .ali file with template (6HUG) and with target sequences. I have received the error: 'There should be 10 fields separated by colons, : This line actually contains 15 fields.' I don't understand how I should correctly change it, if I have 5 chains. Could you please advise, how I should correctly write this 10 field line. I have already read the manual https://salilab.org/modeller/manual/node501.html#alignmentformat, but there is information about 2 chains. I still can not understand how correctly I should write it for 5 chains. The alignment for my template is look like: >P1;6HUG structureX:6HUG:FIRST:A 437:A 473:B 495:C 437:D 473:E:::3.5:-1.00 ------------------------------DYKDDD----DKQPSLQDEL---------K DNTTVFTRILDRLLDGYDNRL---------------RPG----LGERVTEVKTD-IFVTS FGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVA HNMTMPNKLLRITEDGTLLYTMRLTV----RAECPMHLEDFPMDAHACPLKFGSYAYTRA EVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGY FVIQTYLPC---------------IMTVILSQVSFWLNRE-SVPARTV-FGVTTVLTMTT LSISA----RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVP EKPKKVKDPLIKKNN---TY--------------APTA--------TSYT---------- -----------------------------PNLARGD------------------------ ---------------PGLATIAKSATIEPKEVK----------------------PETKP ---------PEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWAT-----YLNREPQLKAP TPHQ----------/ -----MCSGLLEL-------------LLPIWLSWTLGTRGSEPRSV-----------NDP GNMSFVKETVDKLLKGYDIRL---------------RPD----FGGPPVCVGMN-IDIAS IDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFV HGVTVKNRMIRLHPDGTVLYGLRITT----TAACMMDLRRYPLDEQNCTLEIESYGYTTD DIEFYWRGGDKAV--TGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGY FILQTYMPS---------------ILITILSWVSFWINYD-ASAARVA-LGITTVLTMTT INTHL----RETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAE KTAK-AKNDRSKSES--------------------------------------NRVDAHG NILLTSL--E-VHNE---------MNE--VSGGIGD------------------------ ---------------TRNSAISFDNSGI-QYRK-----QSMPREGHGRFLGDRSLPHKKT HLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLY-----YVN-------- --------------/ MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK VPEGDVTVILNNLLEGYDNKL---------------RPD----IGVKPTLIHTD-MYVNS IGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADA HWITTPNRMLRIWNDGRVLYTLRLTI----DAECQLQLHNFPMDEHSCPLEFSSYGYPRE EIVYQWKRSSVEV--GDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGY FTIQTYIPC---------------TLIVVLSWVSFWINKD-AVPARTS-LGITTVLTMTT LSTIA----RKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSNRKPS------K DKDKKKKNPLLRMFS---FK--------------APTI--------D-I----------- -----------------------------------R------------------------ ---------------PRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCFEDCRTGA ---------WRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVS-----YLYLGGSGGSG GSGKTETSQVAPA-/ ------------------------------DYKDDD----DKQPSLQDEL---------K DNTTVFTRILDRLLDGYDNRL---------------RPG----LGERVTEVKTD-IFVTS FGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVA HNMTMPNKLLRITEDGTLLYTMRLTV----RAECPMHLEDFPMDAHACPLKFGSYAYTRA EVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGY FVIQTYLPC---------------IMTVILSQVSFWLNRE-SVPARTV-FGVTTVLTMTT LSISA----RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVP EKPKKVKDPLIKKNN---TY--------------APTA--------TSYT---------- -----------------------------PNLARGD------------------------ ---------------PGLATIAKSATIEPKEVK----------------------PETKP ---------PEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWAT-----YLNREPQLKAP TPHQ----------/ -----MCSGLLEL-------------LLPIWLSWTLGTRGSEPRSV-----------NDP GNMSFVKETVDKLLKGYDIRL---------------RPD----FGGPPVCVGMN-IDIAS IDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFV HGVTVKNRMIRLHPDGTVLYGLRITT----TAACMMDLRRYPLDEQNCTLEIESYGYTTD DIEFYWRGGDKAV--TGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGY FILQTYMPS---------------ILITILSWVSFWINYD-ASAARVA-LGITTVLTMTT INTHL----RETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAE KTAK-AKNDRSKSES--------------------------------------NRVDAHG NILLTSL--E-VHNE---------MNE--VSGGIGD------------------------ ---------------TRNSAISFDNSGI-QYRK-----QSMPREGHGRFLGDRSLPHKKT HLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLY-----YVN-------- --------------* Thank you for your help.

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Missing Residues at the Start, As Well As in the Middle, of the Sequence of a Chain
by Siddhartha Barua 30 May '24

30 May '24

Dear Modeller Discussion Forum Members, I am trying to repair Chain B in the RCSB PDB 5BS8. 5BS8's structure is that of DNA gyrase (from Mycobacterium tuberculosis). I used the example scripts, for filling in missing residues with Modeller, which were given at the URL https://salilab.org/modeller/wiki/Missing_residues (in Modeller Wiki), as well as the "basic-example" tutorial at the main Modeller website, and a YouTube tutorial video for guidance. *Chain B contains 2 missing residues at the start of the sequence associated with the chain in the PDB file- S423 and N424. Thereafter, it contains the sequence "A(425)LVRRK(430)" (with atom records/coordinates) and then a stretch of 6 missing residues- "S(431)ATDIG(436)". *I used the first script given at the abovementioned URL to generate a sequence file extracted from the PDB. *I then used the following as my alignment file (using the NCBI RefSeq (NP_214519.2) for Mycobacterium tuberculosis gyrB (DNA Gyrase subunit B):* >P1;5bs8 structure:5bs8.pdb:FIRST:B:LAST:B:DNA Gyrase::: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALVRRK------GLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV* >P1;5bs8B_fill sequence::::::::: MAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAESTAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV* *I used the following as the script to run AutoModel to model only the selected residues:* from modeller import * from modeller.automodel import * # Load the AutoModel class log.verbose() env = Environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(AutoModel): def select_atoms(self): return Selection(self.residue_range('431:B', '436:B')) a = MyModel(env, alnfile = '5bs8_B-alignment.ali', knowns = '5bs8', sequence = '5bs8B_fill') a.starting_model= 1 a.ending_model = 1 *This then raised the following error:* return Selection(self.residue_range('431:B', '436:B')) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 385, in residue_range start = self.residues[start]._num ~~~~~~~~~~~~~^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 302, in __getitem__ ret = modutil.handle_seq_indx(self, indx, self.mdl._indxres, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\util\modutil.py", line 24, in handle_seq_indx int_indx = lookup_func(*args) ^^^^^^^^^^^^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 379, in _indxres self._report_bad_index(indx, suffix, "residue", 0) File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 372, in _report_bad_index raise KeyError("No such %s: %s" % (indxtyp, indx)) *KeyError: 'No such residue: 431:B'* Next, I tried to run it again after deleting the 424 "-"s that preceded the sequence in the structure-associated sequence portion of the alignment file (>P1;5bs8 structure:5bs8.pdb:FIRST:B:LAST:B:DNA Gyrase:::) and replacing them with 2 "-"s for S423 and N424 and the again, without these 2 preceding "-"s. Both times, I then got the same error: (...... *KeyError: 'No such residue: 431:B'*) *Please advise me on how to fill in missing residues for a chain that (a) has coordinates only for a middle portion/domain of the entire possible sequence (for the full-length protein) (because only the middle portion/domain was crystallised and subjected to X-ray crystallography, say) and (b) has missing residues at the start of this chain (due to high B-factors, say) with respect to the sequence that is associated with the solved structure of the chain in question (as can be seen in PDB viewer softwares such as UCSF Chimera) (e.g.: chain B of RCSB PDB 5BS8).* Thanks, and regards, Siddhartha A. Barua, Ph.D. -- Siddhartha A. Barua, Ph.D. Mb.: +91 7777093994

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coarse parallelization
by Jed Goldstone 16 May '24

16 May '24

I would like to use coarse-grained parallelization with automodel (through slurm) to create (say) 100 models. As Modeller is deterministic, even if I start a job array with different model numbers, each separate job creates the same models. So, for example, if I start job using 4 different python scrips with model ids 0-24, 25-49,50-74, and 75-99, I will get 4 sets of identical models. How can I turn off this deterministic behavior? With thanks, Jed . . Jed Goldstone, PhD Biology Department Woods Hole Oceanographic Institution

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_modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables.
by Rana Rehan Khalid 06 May '24

06 May '24

Dear Modeller Users, I am currently attempting to generate various mutant models using the MutantBuilder script available at https://github.com/eved1018/MutantBuilder. I have installed Modeller10.5 for this purpose. However, I am encountering the following issue: python3 MutantBuilder.py -pdb complex.pdb -c B Traceback (most recent call last): File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 372, in <module> main() File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 368, in main model(pdb, mutants, chain, mutant_name, outfolder) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 188, in HomologyModel mutant_pdb = autoModelPDB(pdb, aln ) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 204, in autoModelPDB a.make() File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 638, in homcsr self.mkhomcsr(Selection(self), aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 716, in mkhomcsr self.build_charmm_restraints(atmsel, rsr, aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 678, in build_charmm_restraints rsr.make(atmsel, aln=aln, restraint_type=type+'_dihedral', File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/restraints.py", line 156, in make return func(self.__mdl.modpt, edat.modpt, aln.modpt, io.modpt, _modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables. Could someone please assist me in resolving this problem? Your help would be greatly appreciated. Best Wishes Rehan

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my automodel run well serial, but molpdf is inmediatly exceeded when run in parallel
by Mario Bianchet 16 Apr '24

16 Apr '24

Hello All The script below exceeds molpdf limits immediately when run this automodel job on parallel, but run starts with a low molpdf and ends well when commenting the line "a.use_parallel_job(j)" Any hint of how to solve will be appreciate? Mario from modelito import MyModel from modeller.parallel import * icycle=50 log.minimal() # request minimal output env = Environ() # create a new MODELLER environment to build this model in icycle=str(int(icycle)+1) # directories for input atom files env.io.atom_files_directory = ['.', 'trajs/'] # Give less weight to all soft-sphere restraints: env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) # Very thorough VTFM optimization: j = Job() for i in range(1): j.append(local_slave()) # Comparative modeling by the AutoModel class env.io.hetatm=True a = MyModel(env, alnfile = 'test.ali', # alignment filename knowns = ('ro','odo'), # codes of the templates sequence = 'TEST') # code of the target a.starting_model= int(icycle) # index of the first model a.ending_model = int(icycle)+ 0 # index of the last model # (determines how many models to calculate) a.library_schedule = autosched.slow #a.restraints.write(file='restraints.rsr') # Thorough MD optimization: a.md_level = refine.slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.use_parallel_job(j) a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() # do the actual comparative modeling

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Re: About the error ( UnicodeDecodeError: 'utf-8' codec can't decode)form logger.py
by Modeller Caretaker 16 Apr '24

16 Apr '24

On 4/16/24 8:22 AM, c00jsw00 wrote: > thanks for your help. When I use win 11 (anaconda powershell) to run a > simple python input and got the error. ... > File "D:\conda\Library\modeller\modlib\modeller\util\logger.py", line 8, > in Logger > _header = _modeller.mod_header_get() > ^^^^^^^^^^^^^^^^^^^^^^^^^^ > UnicodeDecodeError: 'utf-8' codec can't decode byte 0xaa in position > 957: invalid start byte Ah, I see the problem. It is trying to print the start of the Modeller log file, which has information on the Modeller version and environment. Position 957 is about where your computer name is. We assume that name is valid ASCII or UTF8 (and nobody's reported this error before!) but I suppose it doesn't have to be, particularly in non-Western locales. We'll fix this issue for the next Modeller release. In the meantime you could work around it in one of two ways: 1. Change your computer name in Control Panel to something containing only plain ASCII (e.g. try "XXX") and reboot. or 2. Edit logger.py in your Modeller installation, i.e. D:\conda\Library\modeller\modlib\modeller\util\logger.py and change line 8 from _header = _modeller.mod_header_get() to _header = ' ' Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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About the error ( UnicodeDecodeError: 'utf-8' codec can't decode)form logger.py
by c00jsw00＠kmu.edu.tw 15 Apr '24

15 Apr '24

Dear all, When I use conda to install modller 10.4 or 10.5, I used the python (3.9) to run a simple command (from modeller import *). Then I got the error (UnicodeDecodeError: 'utf-8' codec can't decode...) . Could you tell me how to overcome it ? THX YT

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Perodic boundary condition?
by Qizan Chen 05 Apr '24

05 Apr '24

Can the Modeller take periodic boundary conditions into account during modeling? I aim to construct a condensed model, but currently, unwarping the protein to the Modeller and then warping it back leads to incorrect overlaps of side chains. I noticed that symmetry constraints can be added, but my original system is already large, and adding additional images causes crashes.

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Error identifying new atomtypes in $RADII_LIB while adding new residue into modeller topology library
by Neeraj Kumar T . 21 Mar '24

21 Mar '24

I've been trying to add a new residue's (ligand) topology and parameters into modeller library to model accurately. I am following the steps in modeller's FAQ #8: https://salilab.org/modeller/FAQ.html#8. After adding the topology into a copy of "top_heav.lib", and parameters into a copy of "par.lib", and also into copies of "radii.lib" and "solv.lib", I still get errors. This is the initial script I used: ------------------ [image: image.png] -------------------- The above script gives error in the 5th command-line as follows: ------------------------------ *ERROR Case-1:* >>> env.libs.parameters.append(file='$(LIB)/radii_edited.lib') read_pa_233E> No keyword before contents. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.10/dist-packages/modeller/parameters.py", line 25, in append return _modeller.mod_parameters_read(self._modpt, self.__libs.modpt, _modeller.ModellerError: read_pa_233E> No keyword before contents. >>> ------------------------------- Therefore, I deleted command-lines 5&6, and executed the following script. ----------------------------- [image: image.png] ---------------------------------- And executing the above script gave the following error for the 5th command-line: -------------------------------------- *ERROR Case-2:* >>> env.libs.topology.read(file='$(LIB)/top_heav_edited.lib') read_to_681_> topology.submodel read from topology file: 3 read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 23, in read return self.append(file) File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 28, in append return _modeller.mod_topology_read(self._modpt, self.__libs.modpt, _modeller.ModellerError: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O -------------------------------- This happens inspite of the fact that I have added the radii of new atomtypes into "radii.lib" file itself, and not in the copy "radii_edited.lib", as follows: [image: image.png]

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Modelling based on two templates - one oligomer and one monomer
by hmad3＠cam.ac.uk 19 Mar '24

19 Mar '24

Hello, I am trying to model a multichain protein using 2 templates - the .pdb file of an oligomer (with the same number of chains as the target) and the .pdb file of the AlphaFold structure of one of the monomers making up the target protein. (When I model using only the oligomer as target, the model of the target looks quite "off".) First scenario: * target protein: 5 of the same chain * template protein 1 ("base template"): a homopentamer * template protein 2 ("sub-template" - i.e. the target protein is first modelled based on the first template then modelled based on the 2nd template): the AF predicted structure of one chain of the target protein (the .pdb file has only one chain). Second scenario: * target protein: a heteropentamer - 2 of one chain + 3 of another chain * template protein 1: as in the previous scenario * template protein 2 (+3): AF predicted structures of the two chains making up the target heteropentamer. There are 2 AF folds, one for each monomer, each one with a single chain. How would I format the alignment file? I look forward to your guidance. Kind regards, Amanda

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