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

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 18 10:14:20 PST 2012

Hi Steven,
Not to worry, there are many potentially confusing bits here and there! Better to ask than to give up and be disgruntled. As you saw, in the dialog "choose template structure" really meant "choose sequence that is associated with your template structure." I'm glad you got it sorted out -

On Jan 18, 2012, at 3:47 AM, Steven Bottomley wrote:

> Hi Elaine
> Thank you very much for your quick feedback. I had read all the web pages you referred to in your email. However, your email did help me realise I was making a very simple (and embarrassing) mistake. I was using a filename for my template structure that was different from the filename I used for the alignment of the templates's sequence to the target sequence. Consequently, when I chose 'Modeller Tools' from 'MultAlign Viewer' and tried to 'find' my template structure's filename in the 'Choose at least one template' dialog box it wasn't there. The dialog box only contained the name of the template's sequence and the 'structure ID' column was blank. Of course, I had also failed to realise that Chimera had automatically associated the sequence to the structure even though the structure's filename was not listed in the dialog box. I know this sounds a bit weird but thank you for your help!
> Regards
> Steven
> On 18/01/2012, at 1:24 AM, Elaine Meng wrote:
>> 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:
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
>> ... some ways to generate the needed inputs:
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
>> I hope this helps,
>> Elaine
>> ----------
>> 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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