[Chimera-users] Help on using Modeller interface

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 9 16:09:08 PDT 2020

Hi Tiglath,
Are you using ChimeraX (not Chimera)?  It isn't even possible to use all four chains from the same model as the template in Chimera.

However, if the extra chains make you feel confused in either program, a simple approach is to just delete chains B-D from the template structure before modeling.   E.g. open the template structure and then use Chimera command "delete :.B-D" or ChimeraX command "delete /B-D."

Then proceed with modeling as you were before.

If you have ChimeraX questions, for future reference there is a different mailing list: chimerax-users at cgl.ucsf.edu
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 9, 2020, at 3:27 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> Hi
> I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying.
> I would be very grateful for your help.
> Thanks
> Tiglath 

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