[Chimera-users] Using local PDB file for homology modelling

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 17 09:24:49 PST 2012

Hi Steven,
There is no restriction on what structure is used for a template; all you need is a template-target sequence alignment and the template structure both open in Chimera, with the template associated with the sequence.  The second link below explains how to get to that state, starting with your own template structure.

Homology modeling via Chimera:

... some ways to generate the needed inputs:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 16, 2012, at 6:15 PM, Steven Bottomley wrote:

> Hi 
> Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.

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