[chimerax-users] dual conformation

[Wen-Jin Winston Wu]

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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