Re: [modeller_usage] loop refining of a multi chain protein

Dear Sir

Thanks for suggestion ,it worked. After running the script two PDB files are generated one with extension .BL00010001 and other with .IL00000001 extension.Which one should I select and on which basis?

From: Dinesh Babu KR <>
To: subarna thakur <>
Sent: Friday, 29 May, 2009 11:51:19 AM
Subject: Re: [modeller_usage] loop refining of a multi chain protein

hi
in the loop script file you have to mention the chain like this

self.residue_range('77:B', '80:B')

regards,
dinesh

On Fri, May 29, 2009 at 1:49 PM, subarna thakur <" target=_blank rel=nofollow ymailto="mailto:">> wrote:

Dear User

I have a protein with multichain and I am using loop.py script for refining a protein but a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok.

In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script.

Subarna thakur

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