[modeller_usage] Re: Missing Residue and Loop Modeling Script Inquiry for an OLIGOMER

[Joel Subach <>]

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 <
> 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
> --
>              https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>
>

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

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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 ð???

On Sat, Sep 24, 2022 at 12:00 AM Modeller Caretaker <">> 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
--
" target="_blank">             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage