[chimerax-users] dual conformation

[Wen-Jin Winston Wu]

Hi Elaine,

Thanks a lot for the helpful suggestion! I have tried your suggested command
I understand it now that for resfit, the ChimeraX daily build is designed to
display one conformer at a time, but not both of the resfit results for the
two conformers at the same time.

Best wishes,

Winston


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Sunday, June 13, 2021 11:37 PM
To: Wen-Jin Winston Wu <winston at gate.sinica.edu.tw>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] dual conformation

Hi Winston,
In my previous example with two copies (#1 using one altloc for 66 and #2
using the other altloc for 66), you could just specify which copy to resfit,
e.g.

resfit #1/a:66 map #3
 - OR -
resfit #2/a:66 map #3

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 13, 2021, at 12:34 AM, Wen-Jin Winston Wu via ChimeraX-users
<chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Many thanks for your prompt reply and help!
> I have used the daily build "ChimeraX 1.3.dev202106110002", and am 
> able to show the two alternative conformation following your suggested
commands.
> 
> The remaining wish for me is showing the fitted density map onto each 
> of the alternative conformation and have them display simultaneously.
> 
> It seems that the command " resfit /a:66 map #3" only fits one 
> specific conformation. Is there any way that I could specify conformer A
or B?
> Of course, if this is unavailable, I will go back to Chimera 1.15. (I 
> am new to Chimera).
> 
> Best wishes,
> 
> Winston
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Sunday, June 13, 2021 5:25 AM
> To: Wen-Jin Winston Wu <winston at gate.sinica.edu.tw>
> Cc: chimerax-users at cgl.ucsf.edu
> Subject: Re: [chimerax-users] dual conformation
> 
> 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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