[chimerax-users] dual conformation

[Elaine Meng]

Oops, I forgot to include the link to the "altlocs" help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html>

That's the copy at our website.  However, you can also see the help included in your download (ChimeraX 1.3 daily build) using the "help" command, for example:

help altlocs

Best,
Elaine

> On Jun 12, 2021, at 2:25 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Winston,
> ChimeraX is different from Chimera in that it only "uses" (and shows) one alternate location at a time.  This prevents weird behavior in various calculations that can arise from having more than one copy of the same atom (e.g. H-bonding, molecular surface, etc.)  
> 
> However, in recent daily builds there is an "altlocs" command to list these alternate locations and control which one is shown.  This command is not in the 1.2 release, you would need to use a ChimeraX 1.3 daily build from April 28 or later.y
> 
> To see two alternate locations of a residue at the same time, currently you would need to open the structure twice and use the "altlocs" command to change one copy to use the other alternate location.  Example commands:
> 
> open 7a5v
> open 7a5v
> hide
> show :66
> view :66
> altlocs list :66
> 
>   ... Log shows: 
> 7a5v #1/A TYR 66 has alternate locations A and B (using A)
> 7a5v #2/A TYR 66 has alternate locations A and B (using A)
> 
> ...Alternatively, this command would list all of the alternate locations found for all residues:
> 
> altlocs list
> 
> ...Then to change to altloc B of residue 66 in the second copy of your structure:
> 
> altlocs change B #2/A:66
> 
> If you don't care about seeing different altlocs at the same time, you don't need to open multiple copies.  We realize that opening multiple copies can be inconvenient, so we have discussed having a graphical interface and showing the altlocs for a residue all at once (similar to the Rotamers tool showing multiple sidechain rotamers at the same time, and maybe even tabulating H-bonds, clashes, and density fit) but that has not been implemented yet.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 12, 2021, at 9:42 AM, Wen-Jin Winston Wu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi,
>> I am trying to use Chimera X to display an amino acid with dual side chain conformations (PDB code: 7a5v) together with its cryoEM density map (EMDataResource: EMD-11657). 
>> For example, Tyr 66 have two side chain conformations, however using the command below, it only showed one conformation.
>> resfit /a:66 map #1  (a very nice command, by the way)
>> 
>> I then used Chimera 1.15 to view the PDB coordinate, and it showed two side chain conformations for Tyr66 (as I saw in PyMol); on the other hand, Chimera X only shows a single conformation.
>> Is there any way to display the two alternative conformations using Chimera X?
>> 
>> Thanks a lot for your time, and possible help!
>> Best wishes,
>> Winston
> 
> 
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