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Re: [modeller_usage] Loop Modeling using only part of a PDB file

To: Robert Selwyne <>
Subject: Re: [modeller_usage] Loop Modeling using only part of a PDB file
From: Modeller Caretaker <>
Date: Tue, 08 Sep 2009 20:05:50 -0700
Cc:

Robert Selwyne wrote:

Residues from PHE 1223 to LEU 1245 are missing from PDB:2RFN. I want
to use ONLY the residues from 382 to 406 in my template sequence
PDB:3LCK for loop modelling. Remaining part of the residues in the
target shouldnot be disturbed.

(2RFN) Target      : PHE 1223 to LEU 1245 (24 residues)
(3LCK) Template : ASP   382 to TRP  406   (24 residues)

Could you please tell me how to model this?

This is not what Modeller calls "loop modeling"; that is modeling aregion that has no template. To do what you're asking you should usesomething similar to http://salilab.org/modeller/9v7/manual/node23.html


	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

References:
- [modeller_usage] Loop Modeling using only part of a PDB file
  - From: Robert Selwyne <>

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