Dear all,
I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt.
Thanks so much!
Best, Ray
Dear Ray, Sorry no, currently ChimeraX has neither scene saving nor an Animation graphical interface where these scenes can be used as checkpoints.
However, ChimeraX does include the ability to save "views" which include positions of everything, but not their coloring or display settings. You can save and restore views with the "view" command, and the named views are included in saved session files.
You can definitely create very nice animations with ChimeraX command-file (.cxc file) scripting using "view" "2dlabels" and various movement commands, as listed in the Making Movies page in the User Guide: http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
The Making Movies page also includes links to ChimeraX movie-making tutorials and the "morph movie" feature highlight. Several of the feature highlights include the .cxc files used to make 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 May 1, 2020, at 2:48 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray
Dear Elaine,
Thank you for the prompt reply. This is very helpful. I was mostly thinking to save multiple figures' settings in one ChimeraX session. I guess a simple solution for me is to save each figure as different ChimeraX session files.
Thanks again. The "view" command you mentioned can be very useful for making movies -- I will need it soon!
Best, Ray
On Fri, May 1, 2020 at 3:04 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Ray, Sorry no, currently ChimeraX has neither scene saving nor an Animation graphical interface where these scenes can be used as checkpoints.
However, ChimeraX does include the ability to save "views" which include positions of everything, but not their coloring or display settings. You can save and restore views with the "view" command, and the named views are included in saved session files.
You can definitely create very nice animations with ChimeraX command-file (.cxc file) scripting using "view" "2dlabels" and various movement commands, as listed in the Making Movies page in the User Guide: http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
The Making Movies page also includes links to ChimeraX movie-making tutorials and the "morph movie" feature highlight. Several of the feature highlights include the .cxc files used to make 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 May 1, 2020, at 2:48 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear all, I have been searching for the equivalent function in ChimeraX for the
Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt.
Thanks so much! Best, Ray
You're welcome!
Your plan to save a separate session for each figure sounds reasonable. Unless it was only a few commands to convert between the different figures (which one would need to write down or save in a .cxc file for convenience), I would probably do the same thing.
Best, Elaine
On May 1, 2020, at 3:10 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear Elaine,
Thank you for the prompt reply. This is very helpful. I was mostly thinking to save multiple figures' settings in one ChimeraX session. I guess a simple solution for me is to save each figure as different ChimeraX session files.
Thanks again. The "view" command you mentioned can be very useful for making movies -- I will need it soon!
Best, Ray
On Fri, May 1, 2020 at 3:04 PM Elaine Meng meng@cgl.ucsf.edu wrote: Dear Ray, Sorry no, currently ChimeraX has neither scene saving nor an Animation graphical interface where these scenes can be used as checkpoints.
However, ChimeraX does include the ability to save "views" which include positions of everything, but not their coloring or display settings. You can save and restore views with the "view" command, and the named views are included in saved session files.
You can definitely create very nice animations with ChimeraX command-file (.cxc file) scripting using "view" "2dlabels" and various movement commands, as listed in the Making Movies page in the User Guide: http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
The Making Movies page also includes links to ChimeraX movie-making tutorials and the "morph movie" feature highlight. Several of the feature highlights include the .cxc files used to make 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 May 1, 2020, at 2:48 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Forgot to say:
Even when I save a separate session per figure, I also save a view for that figure in the session (use "view name something" command before "save blah.cxs"). That way, if I open the session and then accidentally move something, it's easy to restore the position with a "view something" command rather than having to close the session and reopen it.
Elaine
On May 1, 2020, at 4:04 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
You're welcome!
Your plan to save a separate session for each figure sounds reasonable. Unless it was only a few commands to convert between the different figures (which one would need to write down or save in a .cxc file for convenience), I would probably do the same thing.
Best, Elaine
On May 1, 2020, at 3:10 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear Elaine,
Thank you for the prompt reply. This is very helpful. I was mostly thinking to save multiple figures' settings in one ChimeraX session. I guess a simple solution for me is to save each figure as different ChimeraX session files.
Thanks again. The "view" command you mentioned can be very useful for making movies -- I will need it soon!
Best, Ray
On Fri, May 1, 2020 at 3:04 PM Elaine Meng meng@cgl.ucsf.edu wrote: Dear Ray, Sorry no, currently ChimeraX has neither scene saving nor an Animation graphical interface where these scenes can be used as checkpoints.
However, ChimeraX does include the ability to save "views" which include positions of everything, but not their coloring or display settings. You can save and restore views with the "view" command, and the named views are included in saved session files.
You can definitely create very nice animations with ChimeraX command-file (.cxc file) scripting using "view" "2dlabels" and various movement commands, as listed in the Making Movies page in the User Guide: http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
The Making Movies page also includes links to ChimeraX movie-making tutorials and the "morph movie" feature highlight. Several of the feature highlights include the .cxc files used to make 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 May 1, 2020, at 2:48 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
This is a great idea. Thanks so much, Elaine!
Ray
On Fri, May 1, 2020 at 4:20 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Forgot to say:
Even when I save a separate session per figure, I also save a view for that figure in the session (use "view name something" command before "save blah.cxs"). That way, if I open the session and then accidentally move something, it's easy to restore the position with a "view something" command rather than having to close the session and reopen it.
Elaine
On May 1, 2020, at 4:04 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
You're welcome!
Your plan to save a separate session for each figure sounds reasonable.
Unless it was only a few commands to convert between the different figures (which one would need to write down or save in a .cxc file for convenience), I would probably do the same thing.
Best, Elaine
On May 1, 2020, at 3:10 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Dear Elaine,
Thank you for the prompt reply. This is very helpful. I was mostly
thinking to save multiple figures' settings in one ChimeraX session. I guess a simple solution for me is to save each figure as different ChimeraX session files.
Thanks again. The "view" command you mentioned can be very useful for
making movies -- I will need it soon!
Best, Ray
On Fri, May 1, 2020 at 3:04 PM Elaine Meng meng@cgl.ucsf.edu wrote: Dear Ray, Sorry no, currently ChimeraX has neither scene saving nor an Animation
graphical interface where these scenes can be used as checkpoints.
However, ChimeraX does include the ability to save "views" which
include positions of everything, but not their coloring or display settings. You can save and restore views with the "view" command, and the named views are included in saved session files.
You can definitely create very nice animations with ChimeraX
command-file (.cxc file) scripting using "view" "2dlabels" and various movement commands, as listed in the Making Movies page in the User Guide:
http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
The Making Movies page also includes links to ChimeraX movie-making
tutorials and the "morph movie" feature highlight. Several of the feature highlights include the .cxc files used to make 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 May 1, 2020, at 2:48 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu
wrote:
Dear all, I have been searching for the equivalent function in ChimeraX for the
Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt.
Thanks so much! Best, Ray
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Elaine Meng -
Ray Y.-R. Wang