[chimerax-users] deleting alternate locations

[Elaine Meng]

> On Apr 18, 2023, at 3:07 AM, Yu GUO 郭宇 <guoyu60 at westlake.edu.cn> wrote:
> 
> Dear,
> 
> I am using Chimera/ChimeraX. I have 2 questions:
> 
> I cannot open ChimeraX (win10 version) recently. Is there any problem in the server?
> 
> I have a PDB file with two structural populations. In Chimera, how to delete the part with fewer population (say 40%)? I rememer it can be realized in the command line, but I forgot.
> 
> Best wishes
> 


Dear Sir,
In the future, please use the following addresses (CC'd here) for general questions about the programs:

chimerax-users at cgl.ucsf.edu for ChimeraX questions
chimera-users at cgl.ucsf.edu for Chimera questions

(where you sent this question is for commercial licensing questions -- thanks)

(1) after you download the program, it does not depend on our servers to start. The issue is something with your own setup.  The most likely problem is that you need to update your graphics driver but we would need more information from you to say anything else.

(2) if you mean atomic occupancy, 

- in Chimera you can use Dock Prep (menu: Tools... Structure Editing... Dock Prep) and turn on the option "If alternate locations, keep only highest occupancy".  You can turn off all the other options if you want.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>

- in ChimeraX, it is not currently in the Dock Prep GUI, but you can use the "altlocs clean" command which would delete all the altlocs that are not currently used.  By default, the highest-occupancy ones are the ones that are used, so this would delete the lower-occupancy ones (e.g. your 40%).  You can change which altlocs are used with "altlocs change" and show a list of them with "altlocs list"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html#clean>

If you need a PDB file then you can save PDB in a separate step, e.g. using File menu or a command.

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