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: https://www.emdataresource.org/EMD-11657 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
*************************
ATOM 495 N ATYR A 66 124.799 162.717 112.222 0.50 11.67
N
ATOM 496 N BTYR A 66 125.017 162.760 112.080 0.50 12.99
N
ATOM 497 CA ATYR A 66 124.008 162.914 110.998 0.50 12.05
C
ATOM 498 CA BTYR A 66 124.035 162.916 111.002 0.50 14.20
C
ATOM 499 C ATYR A 66 124.638 164.062 110.190 0.50 11.84
C
ATOM 500 C BTYR A 66 124.433 164.115 110.140 0.50 13.40
C
ATOM 501 O ATYR A 66 125.008 165.077 110.788 0.50 11.86
O
ATOM 502 O BTYR A 66 124.411 165.246 110.660 0.50 14.99
O
ATOM 503 CB ATYR A 66 122.562 163.249 111.355 0.50 13.02
C
ATOM 504 CB BTYR A 66 122.666 163.125 111.624 0.50 17.22
C
ATOM 505 CG ATYR A 66 121.759 162.139 111.997 0.50 14.56
C
ATOM 506 CG BTYR A 66 121.542 163.315 110.654 0.50 21.09
C
ATOM 507 CD1ATYR A 66 121.860 161.839 113.348 0.50 16.21
C
ATOM 508 CD1BTYR A 66 120.718 162.258 110.325 0.50 25.90
C
ATOM 509 CD2ATYR A 66 120.832 161.436 111.248 0.50 17.74
C
ATOM 510 CD2BTYR A 66 121.189 164.579 110.209 0.50 29.25
C
ATOM 511 CE1ATYR A 66 120.974 160.942 113.960 0.50 18.53
C
ATOM 512 CE1BTYR A 66 119.590 162.443 109.543 0.50 32.51
C
ATOM 513 CE2ATYR A 66 119.990 160.494 111.824 0.50 18.57
C
ATOM 514 CE2BTYR A 66 120.067 164.784 109.421 0.50 27.89
C
ATOM 515 CZ ATYR A 66 120.076 160.228 113.177 0.50 20.29
C
ATOM 516 CZ BTYR A 66 119.252 163.714 109.107 0.50 30.80
C
ATOM 517 OH ATYR A 66 119.241 159.287 113.722 0.50 24.21
O
ATOM 518 OH BTYR A 66 118.168 163.886 108.291 0.50 39.05
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
Oops, I forgot to include the link to the "altlocs" help: https://rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html
That's the copy at our website. However, you can also see the help included in your download (ChimeraX 1.3 daily build) using the "help" command, for example:
help altlocs
Best, Elaine
On Jun 12, 2021, at 2:25 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
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
<image1.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
<image1.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 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 <winston@gate.sinica.edu.tw mailto:winston@gate.sinica.edu.tw> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto: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
<image1.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
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Hi Winston,
Oops! Yes I used the "surface zone" command I think but wrote "volume zone" by mistake. But you might want to use "volume zone" and change the "distance 2" option to "range 2" (unfortunately they use different names for that option). The surface zone and volume zone do about the same thing but volume zone is more efficient in that it only computes the mesh for the subregion you are showing while surface zone computes the mesh for the whole map and just hides most of it which can be slow to update when you are trying to change the threshold level.
Also you can set mesh style with the volume command -- that is done by the "style mesh" option in the command I sent (volume #3 style mesh ...).
Tom
On Jun 14, 2021, at 6:07 PM, Wen-Jin Winston Wu winston@gate.sinica.edu.tw wrote:
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.
volume zone help:user/commands/volume.html#zone #3 nearAtoms /a:66 distance 2 Expected a keyword
Best wishes,
Winston
From: Tom Goddard [mailto:goddard@sonic.net mailto:goddard@sonic.net] Sent: Tuesday, June 15, 2021 1:37 AM To: Wen-Jin Winston Wu <winston@gate.sinica.edu.tw mailto:winston@gate.sinica.edu.tw> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto: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 2This 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
TomOn 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 <winston@gate.sinica.edu.tw mailto:winston@gate.sinica.edu.tw> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto: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 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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom,
Thank you so much again!
It works perfectly!
Winston
From: Tom Goddard [mailto:goddard@sonic.net] Sent: Tuesday, June 15, 2021 9:22 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,
Oops! Yes I used the "surface zone" command I think but wrote "volume zone" by mistake. But you might want to use "volume zone" and change the "distance 2" option to "range 2" (unfortunately they use different names for that option). The surface zone and volume zone do about the same thing but volume zone is more efficient in that it only computes the mesh for the subregion you are showing while surface zone computes the mesh for the whole map and just hides most of it which can be slow to update when you are trying to change the threshold level.
Also you can set mesh style with the volume command -- that is done by the "style mesh" option in the command I sent (volume #3 style mesh ...).
Tom
On Jun 14, 2021, at 6:07 PM, Wen-Jin Winston Wu <winston@gate.sinica.edu.tw mailto:winston@gate.sinica.edu.tw > wrote:
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 mailto:goddard@sonic.net] Sent: Tuesday, June 15, 2021 1:37 AM 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,
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 < mailto:chimerax-users@cgl.ucsf.edu 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
< mailto:chimerax-users@cgl.ucsf.edu 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 mailto:meng@cgl.ucsf.edu] Sent: Sunday, June 13, 2021 5:25 AM To: Wen-Jin Winston Wu < mailto:winston@gate.sinica.edu.tw winston@gate.sinica.edu.tw> Cc: mailto:chimerax-users@cgl.ucsf.edu 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
< mailto:chimerax-users@cgl.ucsf.edu 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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participants (3)
-
Elaine Meng -
Tom Goddard -
Wen-Jin Winston Wu