no conformation comparison category in ChimeraX1.5 and ChimeraX-daily
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu
Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu
Sorry, make that "Jiang Xu" not "Jiang Xuf"!! Cold winter fingers cannot type properly. :-)
Elaine
On Dec 12, 2022, at 8:22 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu
Hello Elain, Thanks for your explanation. I am able to create the movie now. I then have two new questions: 1.Following the morph command, I found an arginine residue rotate in a direction that caused clashes with a neighbouring residue in the movement, before moving to the final unclashed position. So is there any way to control the movement direction of the side chain to avoid possible clashes? 2. Now I have the morph trajectory, I also want to have the camera rotate as the structure moves at the same time. Is it possible? Thank you, Best, Jiang
On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX.
I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions?
Thank you, Best, Jiang Xu
Hello Jiang, (1) It is not that easy to control. You could try adding an intermediate structure, e.g. from your first morph, go to some trajectory frame in the middle and manually rotate the arginine to a middle position where you want it to go, then save that as PDB, then reopen as new model. Then to create a new morph trajectory, you would put that new model between your other two models so that the morphing has an additional stage.
To rotate bonds before you save the new model, you could use the "bond rotation" mouse mode to do it interactively with the mouse/touchpad or the "torsion" command to do it with a command (you would probably have to experiment and repeat the command several times and maybe rotate more than one bond in the arginine sidechain to get it where you want). https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html
(2) Morphing creates a new trajectory model. After you create the morph model, you can play it back however you like (go directly to any part, or play multiple times, or back and forth) with the "coordset" command. Overall rotation is done with "turn" or "roll" command.
If you want to make a fancier movie with morphing, normally you would just do the morphing once and then save the session, and then use the session with a command script that controls what the movie shows, as well as "movie record" to start recording after any setup is done and "movie encode" at the end to save the movie, What the movie shows would include "coordset" to play back the morphing results, "turn" or "roll" to rotate the whole structure, and possibly several other things: showing/hiding, displaying title text, changing colors, etc. See "making movies" and links therein to movie-related commands: https://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Command files: https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
Both of these movie tutorials include morphing: https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html
It usually takes a lot of trial and error and executing the command script over and over (even for me) to get it just how you like it. To make "coordset" and "roll" commands happen at the same time, put them next to each other without any "wait" command between them. Example:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2 frames 120 play false turn y -60 movie record coordset #3 loop 3 bounce true; roll x 0.5 726; wait 726 movie encode ~/Desktop/junk.mp4
Several of the commands have lots of options (e.g. loop or bounce in coordset command) and you will need to look at their help pages and spend some time trying them.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 14, 2022, at 5:09 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Elain, Thanks for your explanation. I am able to create the movie now. I then have two new questions: 1.Following the morph command, I found an arginine residue rotate in a direction that caused clashes with a neighbouring residue in the movement, before moving to the final unclashed position. So is there any way to control the movement direction of the side chain to avoid possible clashes? 2. Now I have the morph trajectory, I also want to have the camera rotate as the structure moves at the same time. Is it possible? Thank you, Best, Jiang
On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu
While you can try to reduce clashes during a morph using the method Elaine suggested, be aware that morphing does not take clashes into account in any way say they are extremely common -- usually hundreds or thousands of atom pairs clash in a morph -- since it is just interpolating the conformations. It is not intended to be a realistic motion. It just shows the difference between the conformations in an easy to grasp way.
Tom
On Dec 14, 2022, at 6:15 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Jiang, (1) It is not that easy to control. You could try adding an intermediate structure, e.g. from your first morph, go to some trajectory frame in the middle and manually rotate the arginine to a middle position where you want it to go, then save that as PDB, then reopen as new model. Then to create a new morph trajectory, you would put that new model between your other two models so that the morphing has an additional stage.
To rotate bonds before you save the new model, you could use the "bond rotation" mouse mode to do it interactively with the mouse/touchpad or the "torsion" command to do it with a command (you would probably have to experiment and repeat the command several times and maybe rotate more than one bond in the arginine sidechain to get it where you want). https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html
(2) Morphing creates a new trajectory model. After you create the morph model, you can play it back however you like (go directly to any part, or play multiple times, or back and forth) with the "coordset" command. Overall rotation is done with "turn" or "roll" command.
If you want to make a fancier movie with morphing, normally you would just do the morphing once and then save the session, and then use the session with a command script that controls what the movie shows, as well as "movie record" to start recording after any setup is done and "movie encode" at the end to save the movie, What the movie shows would include "coordset" to play back the morphing results, "turn" or "roll" to rotate the whole structure, and possibly several other things: showing/hiding, displaying title text, changing colors, etc. See "making movies" and links therein to movie-related commands: https://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Command files: https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
Both of these movie tutorials include morphing: https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html
It usually takes a lot of trial and error and executing the command script over and over (even for me) to get it just how you like it. To make "coordset" and "roll" commands happen at the same time, put them next to each other without any "wait" command between them. Example:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2 frames 120 play false turn y -60 movie record coordset #3 loop 3 bounce true; roll x 0.5 726; wait 726 movie encode ~/Desktop/junk.mp4
Several of the commands have lots of options (e.g. loop or bounce in coordset command) and you will need to look at their help pages and spend some time trying them.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 14, 2022, at 5:09 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Elain, Thanks for your explanation. I am able to create the movie now. I then have two new questions: 1.Following the morph command, I found an arginine residue rotate in a direction that caused clashes with a neighbouring residue in the movement, before moving to the final unclashed position. So is there any way to control the movement direction of the side chain to avoid possible clashes? 2. Now I have the morph trajectory, I also want to have the camera rotate as the structure moves at the same time. Is it possible? Thank you, Best, Jiang
On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine and Tom, Thank you for your suggestions and explanations in detail. I want to show my structure in a more intuitive way, even though it may not represent the true process that happened in liquid. I then have a question about measuring torsion angles. I have no problem practicing the example in the tutorial with only one structure. However, when there's multiple structures,say #1 and #2, how to measure torsion angle correctly? The following is an example that I got a mistake: Command: torsion :#1/A:33@n,ca,c,o Missing or invalid "atom" argument: invalid atoms specifier Command: select #1/A:33@n,ca,c,o 4 atoms, 3bonds, 1residue, 1 model selected How to solve this problem? Thanks, Jiang
On Wed, Dec 14, 2022 at 6:51 PM Tom Goddard goddard@sonic.net wrote:
While you can try to reduce clashes during a morph using the method Elaine suggested, be aware that morphing does not take clashes into account in any way say they are extremely common -- usually hundreds or thousands of atom pairs clash in a morph -- since it is just interpolating the conformations. It is not intended to be a realistic motion. It just shows the difference between the conformations in an easy to grasp way.
TomOn Dec 14, 2022, at 6:15 PM, Elaine Meng via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello Jiang, (1) It is not that easy to control. You could try adding an intermediate
structure, e.g. from your first morph, go to some trajectory frame in the middle and manually rotate the arginine to a middle position where you want it to go, then save that as PDB, then reopen as new model. Then to create a new morph trajectory, you would put that new model between your other two models so that the morphing has an additional stage.
To rotate bonds before you save the new model, you could use the "bond
rotation" mouse mode to do it interactively with the mouse/touchpad or the "torsion" command to do it with a command (you would probably have to experiment and repeat the command several times and maybe rotate more than one bond in the arginine sidechain to get it where you want).
https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html
(2) Morphing creates a new trajectory model. After you create the morph
model, you can play it back however you like (go directly to any part, or play multiple times, or back and forth) with the "coordset" command. Overall rotation is done with "turn" or "roll" command.
If you want to make a fancier movie with morphing, normally you would
just do the morphing once and then save the session, and then use the session with a command script that controls what the movie shows, as well as "movie record" to start recording after any setup is done and "movie encode" at the end to save the movie, What the movie shows would include "coordset" to play back the morphing results, "turn" or "roll" to rotate the whole structure, and possibly several other things: showing/hiding, displaying title text, changing colors, etc. See "making movies" and links therein to movie-related commands:
https://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Command files: <
https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...
Both of these movie tutorials include morphing: <https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html
https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html
It usually takes a lot of trial and error and executing the command
script over and over (even for me) to get it just how you like it. To make "coordset" and "roll" commands happen at the same time, put them next to each other without any "wait" command between them. Example:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2 frames 120 play false turn y -60 movie record coordset #3 loop 3 bounce true; roll x 0.5 726; wait 726 movie encode ~/Desktop/junk.mp4
Several of the commands have lots of options (e.g. loop or bounce in
coordset command) and you will need to look at their help pages and spend some time trying them.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 14, 2022, at 5:09 PM, Jiang Xu via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello Elain, Thanks for your explanation. I am able to create the movie now. I then
have two new questions:
1.Following the morph command, I found an arginine residue rotate in a
direction that caused clashes with a neighbouring residue in the movement, before moving to the final unclashed position. So is there any way to control the movement direction of the side chain to avoid possible clashes?
- Now I have the morph trajectory, I also want to have the camera
rotate as the structure moves at the same time. Is it possible?
Thank you, Best, Jiang
On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to
ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions?
Thank you, Best, Jiang Xu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Jiang, The specification is wrong in your torsion command. There should not be any ":" before the model number "#1":
torsion :#1/A:33@n,ca,c,o
should instead be something like
torsion #1/A:33@n,ca,c,o
... just like in your select command.
I hope this helps, Elaine
On Dec 14, 2022, at 7:35 PM, Jiang Xu foxjuly@gmail.com wrote:
Hi Elaine and Tom, Thank you for your suggestions and explanations in detail. I want to show my structure in a more intuitive way, even though it may not represent the true process that happened in liquid. I then have a question about measuring torsion angles. I have no problem practicing the example in the tutorial with only one structure. However, when there's multiple structures,say #1 and #2, how to measure torsion angle correctly? The following is an example that I got a mistake: Command: torsion :#1/A:33@n,ca,c,o Missing or invalid "atom" argument: invalid atoms specifier Command: select #1/A:33@n,ca,c,o 4 atoms, 3bonds, 1residue, 1 model selected How to solve this problem? Thanks, Jiang
On Wed, Dec 14, 2022 at 6:51 PM Tom Goddard goddard@sonic.net wrote: While you can try to reduce clashes during a morph using the method Elaine suggested, be aware that morphing does not take clashes into account in any way say they are extremely common -- usually hundreds or thousands of atom pairs clash in a morph -- since it is just interpolating the conformations. It is not intended to be a realistic motion. It just shows the difference between the conformations in an easy to grasp way.
TomOn Dec 14, 2022, at 6:15 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Jiang, (1) It is not that easy to control. You could try adding an intermediate structure, e.g. from your first morph, go to some trajectory frame in the middle and manually rotate the arginine to a middle position where you want it to go, then save that as PDB, then reopen as new model. Then to create a new morph trajectory, you would put that new model between your other two models so that the morphing has an additional stage.
To rotate bonds before you save the new model, you could use the "bond rotation" mouse mode to do it interactively with the mouse/touchpad or the "torsion" command to do it with a command (you would probably have to experiment and repeat the command several times and maybe rotate more than one bond in the arginine sidechain to get it where you want). https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html
(2) Morphing creates a new trajectory model. After you create the morph model, you can play it back however you like (go directly to any part, or play multiple times, or back and forth) with the "coordset" command. Overall rotation is done with "turn" or "roll" command.
If you want to make a fancier movie with morphing, normally you would just do the morphing once and then save the session, and then use the session with a command script that controls what the movie shows, as well as "movie record" to start recording after any setup is done and "movie encode" at the end to save the movie, What the movie shows would include "coordset" to play back the morphing results, "turn" or "roll" to rotate the whole structure, and possibly several other things: showing/hiding, displaying title text, changing colors, etc. See "making movies" and links therein to movie-related commands: https://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Command files: https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
Both of these movie tutorials include morphing: https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html
It usually takes a lot of trial and error and executing the command script over and over (even for me) to get it just how you like it. To make "coordset" and "roll" commands happen at the same time, put them next to each other without any "wait" command between them. Example:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2 frames 120 play false turn y -60 movie record coordset #3 loop 3 bounce true; roll x 0.5 726; wait 726 movie encode ~/Desktop/junk.mp4
Several of the commands have lots of options (e.g. loop or bounce in coordset command) and you will need to look at their help pages and spend some time trying them.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 14, 2022, at 5:09 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Elain, Thanks for your explanation. I am able to create the movie now. I then have two new questions: 1.Following the morph command, I found an arginine residue rotate in a direction that caused clashes with a neighbouring residue in the movement, before moving to the final unclashed position. So is there any way to control the movement direction of the side chain to avoid possible clashes? 2. Now I have the morph trajectory, I also want to have the camera rotate as the structure moves at the same time. Is it possible? Thank you, Best, Jiang
On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Thank you for your quick response. Best, Jiang
On Wed, Dec 14, 2022 at 7:46 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Jiang, The specification is wrong in your torsion command. There should not be any ":" before the model number "#1":
torsion :#1/A:33@n,ca,c,o
should instead be something like
torsion #1/A:33@n,ca,c,o
... just like in your select command.
I hope this helps, Elaine
On Dec 14, 2022, at 7:35 PM, Jiang Xu foxjuly@gmail.com wrote:
Hi Elaine and Tom, Thank you for your suggestions and explanations in detail. I want to
show my structure in a more intuitive way, even though it may not represent the true process that happened in liquid. I then have a question about measuring torsion angles. I have no problem practicing the example in the tutorial with only one structure. However, when there's multiple structures,say #1 and #2, how to measure torsion angle correctly? The following is an example that I got a mistake:
Command: torsion :#1/A:33@n,ca,c,o Missing or invalid "atom" argument: invalid atoms specifier Command: select #1/A:33@n,ca,c,o 4 atoms, 3bonds, 1residue, 1 model selected How to solve this problem? Thanks, Jiang
On Wed, Dec 14, 2022 at 6:51 PM Tom Goddard goddard@sonic.net wrote: While you can try to reduce clashes during a morph using the method
Elaine suggested, be aware that morphing does not take clashes into account in any way say they are extremely common -- usually hundreds or thousands of atom pairs clash in a morph -- since it is just interpolating the conformations. It is not intended to be a realistic motion. It just shows the difference between the conformations in an easy to grasp way.
TomOn Dec 14, 2022, at 6:15 PM, Elaine Meng via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello Jiang, (1) It is not that easy to control. You could try adding an
intermediate structure, e.g. from your first morph, go to some trajectory frame in the middle and manually rotate the arginine to a middle position where you want it to go, then save that as PDB, then reopen as new model. Then to create a new morph trajectory, you would put that new model between your other two models so that the morphing has an additional stage.
To rotate bonds before you save the new model, you could use the "bond
rotation" mouse mode to do it interactively with the mouse/touchpad or the "torsion" command to do it with a command (you would probably have to experiment and repeat the command several times and maybe rotate more than one bond in the arginine sidechain to get it where you want).
https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html
(2) Morphing creates a new trajectory model. After you create the
morph model, you can play it back however you like (go directly to any part, or play multiple times, or back and forth) with the "coordset" command. Overall rotation is done with "turn" or "roll" command.
If you want to make a fancier movie with morphing, normally you would
just do the morphing once and then save the session, and then use the session with a command script that controls what the movie shows, as well as "movie record" to start recording after any setup is done and "movie encode" at the end to save the movie, What the movie shows would include "coordset" to play back the morphing results, "turn" or "roll" to rotate the whole structure, and possibly several other things: showing/hiding, displaying title text, changing colors, etc. See "making movies" and links therein to movie-related commands:
https://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Command files: <
https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...
Both of these movie tutorials include morphing: <
https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html%3E
https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html
It usually takes a lot of trial and error and executing the command
script over and over (even for me) to get it just how you like it. To make "coordset" and "roll" commands happen at the same time, put them next to each other without any "wait" command between them. Example:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2 frames 120 play false turn y -60 movie record coordset #3 loop 3 bounce true; roll x 0.5 726; wait 726 movie encode ~/Desktop/junk.mp4
Several of the commands have lots of options (e.g. loop or bounce in
coordset command) and you will need to look at their help pages and spend some time trying them.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 14, 2022, at 5:09 PM, Jiang Xu via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello Elain, Thanks for your explanation. I am able to create the movie now. I
then have two new questions:
1.Following the morph command, I found an arginine residue rotate in
a direction that caused clashes with a neighbouring residue in the movement, before moving to the final unclashed position. So is there any way to control the movement direction of the side chain to avoid possible clashes?
- Now I have the morph trajectory, I also want to have the camera
rotate as the structure moves at the same time. Is it possible?
Thank you, Best, Jiang
On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng meng@cgl.ucsf.edu
wrote:
Hi Jiang Xuf, ChimeraX has a "morph" command (not a tool dialog), see:
https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html
Example:
open 2gbp open 2fw0 matchmaker #2 to #1 morph #1,2
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to
ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions?
Thank you, Best, Jiang Xu
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participants (3)
-
Elaine Meng -
Jiang Xu -
Tom Goddard