[Chimera-users] Help on using Modeller interface

[Elaine Meng]

Hi Tiglath,
For the Modeller interface, if you are modeling a monomer, I believe the calculation is the same using Chimera as when using ChimeraX, so no need to switch for that purpose.

However, ChimeraX is our newer program being developed now, and it has several advantages over Chimera, including features that Chimera does not have.  A few are mentioned here:
<http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>

However, it does not yet have all the commonly used features of Chimera, so which program is the best currently depends on exactly what you are trying to do.  Some missing features are listed in the ChimeraX download page (click the triangle to the left of "Missing Features" to see that section):
<http://www.rbvi.ucsf.edu/chimerax/download.html>

Of course, it is perfectly fine to have both programs on your computer and just use them both, depending on the task.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 9, 2020, at 4:13 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> 
> Hi Elaine
> 
> Yes it does. Thanks! I'm using Chimera. Is it better to use ChimeraX?
> 
> 
> Thanks
> 
> Tiglath
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, October 9, 2020 4:09 PM
> To: Moradkhan, Tiglath A <tmoradkhan at csus.edu>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Help on using Modeller interface
>  
> 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
> -----
> 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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