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 firstname.lastname@example.org To: subarna thakur email@example.com 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
On Fri, May 29, 2009 at 1:49 PM, subarna thakur firstname.lastname@example.org 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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subarna thakur wrote: > 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?
The generated loop models have the .BL extension. The .IL files are initial loops, which are unoptimized - you don't want to select those.
Ben Webb, Modeller Caretaker