[chimerax-users] dual conformation

Mon Jun 14 18:07:15 PDT 2021

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 at sonic.net] 
Sent: Tuesday, June 15, 2021 1:37 AM
To: Wen-Jin Winston Wu <winston at gate.sinica.edu.tw>
Cc: ChimeraX Users Help <chimerax-users at 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 at cgl.ucsf.edu <mailto: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 < <mailto:winston at gate.sinica.edu.tw>
winston at gate.sinica.edu.tw>
Cc: ChimeraX Users Help < <mailto:chimerax-users at cgl.ucsf.edu>
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 <mailto: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
<mailto:winston at gate.sinica.edu.tw> >
Cc: chimerax-users at cgl.ucsf.edu <mailto: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 <mailto: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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