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

[Modeller Caretaker <>]

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/
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