[chimerax-users] dual conformation

[Elaine Meng]

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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