Dear ChimeraX users ! Using the following command, I generated a 200-frame trajectory that morphs through three selected conformations: morph #2,3,4 core 0.1 frames 200 wrap f rate linear Would it be possible to have the morphing trajectory end on the starting structure (so the full transition path ends on the first snapshot in the morphin trajectory), so that I can create a smoothly looped GIF animation? Many thanks in advance ! Enrico
The suggestion in the help page is to open the model twice (for example, two copies of same model open as both #2 and #5) and then put both numbers in the morph command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> "For a more complicated trajectory that visits the same conformation more than once, another approach is to open a given structure multiple times to give copies with different model numbers." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 18, 2025, at 3:57 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users !
Using the following command, I generated a 200-frame trajectory that morphs through three selected conformations:
morph #2,3,4 core 0.1 frames 200 wrap f rate linear
Would it be possible to have the morphing trajectory end on the starting structure (so the full transition path ends on the first snapshot in the morphin trajectory), so that I can create a smoothly looped GIF animation?
Many thanks in advance !
Enrico
Thank you very much Elaine ! Specifically I try to visualize the full rotation cycle of ATP synthase using three structures: 5are, 5ari & 5fil If I copy the second one as #5 and the third one as #6 and then executing: morph #2,3,4,5,6 core 0.1 frames 75 wrap f rate linear I have rotation in one side and then in the opposite side in one trajectory. In my project, I would like to make a rotation in one direction but reproducing the full cycle in order that hte final snapshot was the same as the first one, I also tried something like: morph #2,3,4,3,2 core 0.1 frames 75 wrap f rate linear But the end frame was not like the first one . Many thanks in advance Enrico Il giorno ven 18 apr 2025 alle ore 17:55 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
The suggestion in the help page is to open the model twice (for example, two copies of same model open as both #2 and #5) and then put both numbers in the morph command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
"For a more complicated trajectory that visits the same conformation more than once, another approach is to open a given structure multiple times to give copies with different model numbers."
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 18, 2025, at 3:57 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users !
Using the following command, I generated a 200-frame trajectory that morphs through three selected conformations:
morph #2,3,4 core 0.1 frames 200 wrap f rate linear
Would it be possible to have the morphing trajectory end on the starting structure (so the full transition path ends on the first snapshot in the morphin trajectory), so that I can create a smoothly looped GIF animation?
Many thanks in advance !
Enrico
You cannot use the same model number twice in the morph command. As explained in the previous message, you have to open the same structure multiple times and use different model numbers only. So if you want model 1 -> 2 -> 3 -> 1, I believe that you have to open #1 two times so that the second copy is #4 and then use #1,2,3,4 in the command. Elaine
On Apr 19, 2025, at 12:00 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine !
Specifically I try to visualize the full rotation cycle of ATP synthase using three structures: 5are, 5ari & 5fil If I copy the second one as #5 and the third one as #6 and then executing:
morph #2,3,4,5,6 core 0.1 frames 75 wrap f rate linear
I have rotation in one side and then in the opposite side in one trajectory.
In my project, I would like to make a rotation in one direction but reproducing the full cycle in order that hte final snapshot was the same as the first one, I also tried something like:
morph #2,3,4,3,2 core 0.1 frames 75 wrap f rate linear
But the end frame was not like the first one .
Many thanks in advance
Enrico
Il giorno ven 18 apr 2025 alle ore 17:55 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: The suggestion in the help page is to open the model twice (for example, two copies of same model open as both #2 and #5) and then put both numbers in the morph command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
"For a more complicated trajectory that visits the same conformation more than once, another approach is to open a given structure multiple times to give copies with different model numbers."
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 18, 2025, at 3:57 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users !
Using the following command, I generated a 200-frame trajectory that morphs through three selected conformations:
morph #2,3,4 core 0.1 frames 200 wrap f rate linear
Would it be possible to have the morphing trajectory end on the starting structure (so the full transition path ends on the first snapshot in the morphin trajectory), so that I can create a smoothly looped GIF animation?
Many thanks in advance !
Enrico
participants (2)
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Elaine Meng -
Enrico Martinez