Hi Siddhartha I hope your well:).
I superficially scanned your inquiry and I successfully completed missing residue modeling via Modeller via the below link, accordingly if you follow this link step-by-step you should be able to successfully build these missing residues (if you try it maybe again and it does not function feel free to inquire further and I will assist-you:).)
Best, Joel
On Wed, May 29, 2024 at 8:49 AM Siddhartha Barua via modeller_usage < modeller_usage@salilab.org> wrote:
> 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 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/