May 2024 - modeller_usage

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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