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[modeller_usage] Re: Missing Residues at the Start, As Well As in the Middle, of the Sequence of a Chain

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 <
> 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
> 
> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/
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 ð???

On Wed, May 29, 2024 at 8:49â?¯AM Siddhartha Barua via modeller_usage <">> 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
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