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@cgl.ucsf.edu] Sent: Sunday, June 13, 2021 11:37 PM To: Wen-Jin Winston Wu <winston@gate.sinica.edu.tw> Cc: ChimeraX Users Help <chimerax-users@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@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@cgl.ucsf.edu] Sent: Sunday, June 13, 2021 5:25 AM To: Wen-Jin Winston Wu <winston@gate.sinica.edu.tw> Cc: chimerax-users@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@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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