Hi Tom, Thank you so much for the amazing help! So is Elaine's help. I've followed your commands, and the only place that I had to modify replacing "volume zone #3 near /A:66 distance 2" with "surface zone #3 near /a:66 distance 2" that you have suggested. I only had to easily change the display from surface to mesh in the volume viewer. The reason is that ChimeraX instructed me, as shown below, that a keyword was expected with the volume zone and distance 2 as shown below. <help:user/commands/volume.html#zone> volume zone #3 nearAtoms /a:66 distance 2 Expected a keyword Best wishes, Winston From: Tom Goddard [mailto:goddard@sonic.net] Sent: Tuesday, June 15, 2021 1:37 AM 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, Yes, you are right that resfit only shows one conformation. It would be nice it it could show more than one. If you use two copies of the atomic model as Elaine suggests you can easily have it show the density around both, but not with resfit. Instead just give the command to show the zone surface zone #3 near /a:66 distance 2 This will show the map zone around #1 and #2 residue 66. Here are the commands I used to make the image below. open 7a5v open 7a5v hide #1,2 atoms,cartoon show /a:66 view altlocs change B #2/A:66 open 11657 from emdb volume zone #3 near /A:66 distance 2 volume #3 style mesh level 0.025 subdividesurface true Tom On Jun 13, 2021, at 9:04 AM, Wen-Jin Winston Wu via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> > wrote: 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> mailto:meng@cgl.ucsf.edu] Sent: Sunday, June 13, 2021 11:37 PM To: Wen-Jin Winston Wu < <mailto:winston@gate.sinica.edu.tw> winston@gate.sinica.edu.tw> Cc: ChimeraX Users Help < <mailto:chimerax-users@cgl.ucsf.edu> 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 <mailto: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 <mailto:winston@gate.sinica.edu.tw> > Cc: chimerax-users@cgl.ucsf.edu <mailto: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 <mailto: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 <image1.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list <mailto:ChimeraX-users@cgl.ucsf.edu> ChimeraX-users@cgl.ucsf.edu Manage subscription: <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
