Missing Residue and Loop Modeling Script Inquiry for an OLIGOMER
Hello, for the above topic I have a heptamer, accordingly should my missing residue code for chains A-G be just and A-chain indication with the B-G being modeled via default or should I designate each chain, see below:
return Selection(self.residue_range(`88:A´, `100:A´))
or
return Selection(self.residue_range('88:A', '100:A'), self.residue_range('88:B', '100:B'), self.residue_range('88:C', '100:C'), self.residue_range('88:D', '100:D'), self.residue_range('88:E', '100:E'), self.residue_range('88:F', '100:F'), self.residue_range('88:G', '100:G'))
I tried the later (A-G coding) and received the below error where there should be this missing residue?
*raise KeyError("No such %s: %s" % (indxtyp, indx))* *KeyError: 'No such residue: 88:B'*
On 9/23/22 4:52 AM, Joel Subach via modeller_usage wrote: > Hello, for the above topic I have a heptamer, accordingly should my > missing residue > code for chains A-G be just and A-chain indication with the B-G being > modeled via default or should I designate each chain, see below: > > return Selection(self.residue_range(`88:A´, `100:A´))
This will just refine the loop in the A chain.
> return Selection(self.residue_range('88:A', '100:A'), > self.residue_range('88:B', '100:B'), > self.residue_range('88:C', '100:C'), > self.residue_range('88:D', '100:D'), > self.residue_range('88:E', '100:E'), > self.residue_range('88:F', '100:F'), > self.residue_range('88:G', '100:G')) > > I tried the later (A-G coding) and received the below error where there > should be this missing residue? > * > * > *raise KeyError("No such %s: %s" % (indxtyp, indx)) > * > *KeyError: 'No such residue: 88:B'*
You are probably assuming that Modeller numbers the residues in each chain starting from 1. It doesn't by default, although you can ask it to do so: https://salilab.org/modeller/10.3/manual/node30.html
Ben Webb, Modeller Caretaker
Hello Ben thank you for your kind update:).
No I have taken this into account i.e. starting residue is 2 accordingly my starting missing residue is 89 so I made it 88.
Please let me know at least then which of the above I should be using for an oligomer meaning should i designate each chain? (I will take care of the rest of the analysis to manage your time.)
Thanks Ben:) Joel
On Sat, Sep 24, 2022 at 12:00 AM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 9/23/22 4:52 AM, Joel Subach via modeller_usage wrote: > > Hello, for the above topic I have a heptamer, accordingly should my > > missing residue > > code for chains A-G be just and A-chain indication with the B-G being > > modeled via default or should I designate each chain, see below: > > > > return Selection(self.residue_range(`88:A´, `100:A´)) > > This will just refine the loop in the A chain. > > > return Selection(self.residue_range('88:A', '100:A'), > > self.residue_range('88:B', '100:B'), > > self.residue_range('88:C', '100:C'), > > self.residue_range('88:D', '100:D'), > > self.residue_range('88:E', '100:E'), > > self.residue_range('88:F', '100:F'), > > self.residue_range('88:G', '100:G')) > > > > I tried the later (A-G coding) and received the below error where there > > should be this missing residue? > > * > > * > > *raise KeyError("No such %s: %s" % (indxtyp, indx)) > > * > > *KeyError: 'No such residue: 88:B'* > > You are probably assuming that Modeller numbers the residues in each > chain starting from 1. It doesn't by default, although you can ask it to > do so: > https://salilab.org/modeller/10.3/manual/node30.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > >
...and I solved this problem:
when missing residue modeling an oligomer while restraining non-missing residues, the script must be run twice while changing the self residue range in the script subsequent to the generation of the fill.ini file since this file does not start the residue count over for new chains hence the error of: no such residue: 88.B since it needs to be renamed which in this instance is residue # 521.
On Sat, Sep 24, 2022 at 9:44 AM Joel Subach mjsubach@ncsu.edu wrote:
> Hello Ben thank you for your kind update:). > > No I have taken this into account i.e. starting residue is 2 accordingly > my starting missing residue is 89 so I made it 88. > > Please let me know at least then which of the above I should be using for > an oligomer meaning should i designate each chain? > (I will take care of the rest of the analysis to manage your time.) > > Thanks Ben:) > Joel > > On Sat, Sep 24, 2022 at 12:00 AM Modeller Caretaker < > modeller-care@salilab.org> wrote: > >> On 9/23/22 4:52 AM, Joel Subach via modeller_usage wrote: >> > Hello, for the above topic I have a heptamer, accordingly should my >> > missing residue >> > code for chains A-G be just and A-chain indication with the B-G being >> > modeled via default or should I designate each chain, see below: >> > >> > return Selection(self.residue_range(`88:A´, `100:A´)) >> >> This will just refine the loop in the A chain. >> >> > return Selection(self.residue_range('88:A', '100:A'), >> > self.residue_range('88:B', '100:B'), >> > self.residue_range('88:C', '100:C'), >> > self.residue_range('88:D', '100:D'), >> > self.residue_range('88:E', '100:E'), >> > self.residue_range('88:F', '100:F'), >> > self.residue_range('88:G', '100:G')) >> > >> > I tried the later (A-G coding) and received the below error where >> there >> > should be this missing residue? >> > * >> > * >> > *raise KeyError("No such %s: %s" % (indxtyp, indx)) >> > * >> > *KeyError: 'No such residue: 88:B'* >> >> You are probably assuming that Modeller numbers the residues in each >> chain starting from 1. It doesn't by default, although you can ask it to >> do so: >> https://salilab.org/modeller/10.3/manual/node30.html >> >> Ben Webb, Modeller Caretaker >> -- >> modeller-care@salilab.org https://salilab.org/modeller/ >> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >> >>
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Joel Subach -
Modeller Caretaker