[Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 3 16:00:11 PST 2012


I forgot to say:  you should use Chimera version 1.7 for these calculations.  The Modeller interface has been improved since version 1.6, and the manual and tutorial links below describe version 1.7.  

Chimera 1.7 is available as snapshot and daily builds:
<http://www.cgl.ucsf.edu/chimera/download.html#snapshots>
<http://www.cgl.ucsf.edu/chimera/download.html#daily>

Best,
Elaine


On Dec 3, 2012, at 3:56 PM, Elaine Meng wrote:

> Hi Tao Zhao,
> Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program.  To use this feature, you would first need to go to the Modeller web site and sign up for  a license key <http://www.salilab.org/modeller/registration.html>  -- it is free for noncommercial use.
> 
> A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see:
> 
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
> 
> ... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template":
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
> 
> There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
> 
> 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
> 
> P.S. better to send questions about using Chimera to chimera-users at cgl.ucsf.edu (CC'd on this message), not chimera-dev at cgl.ucsf.edu which is meant for programmers
> 
> On Dec 2, 2012, at 10:21 PM, tao zhao wrote:
> 
>> Hello,
>> I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family.
>> It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next.
>> 
>> Could you please give me some instruction?
>> Thank you very much.
>> 
>> Tao Zhao
>> Northwest A&F University,Yangling, China
> 
> 
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