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