*https://salilab.org/modeller/wiki/Missing_residues https://salilab.org/modeller/wiki/Missing_residues*
On Wed, May 29, 2024 at 8:57 AM Joel Subach mjsubach@alumni.ncsu.edu wrote:
> 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/ > >