[chimerax-users] dual conformation

Tom Goddard goddard at sonic.net
Mon Jun 14 10:37:16 PDT 2021 

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 at 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 at cgl.ucsf.edu <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 <mailto:winston at gate.sinica.edu.tw>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto: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
>> 
>> <image1.png>_______________________________________________
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