Saving volumes from volume morphs
Hi, I wanted to ask if there is a way to save each frame of a volume morph through the command line, or if a feature like this could be added? I would like to use each frame of the volume morph series (as .mrc) to export into an external program, but the only way I've found at the moment is to manually change each frame in the morph slider then save that frame. It doesn't appear there is the same coordset slider functionality of the volume morph slider for atomic models, which would be really handy in my situation if the morph has lots of steps. Many thanks Jack
Hi Jack, My understanding is that unlike an atomic morph which is calculated as a trajectory (multiple coordinate sets), the intermediates of a volume morph are not all saved in memory at the same time because each one can be quite large. So there isn't a single command that could save them all at the same time. However, you may be able to use the "volume morph" command to do the same thing you are now doing manually, by including the "playRange" option to halt the morph at a particular stage, then using "save" to save a map, then using "volume morph" again with a different "playRange" [... etc. ...] It may be rather tedious but possibly better than moving the slider by hand. See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> 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 Feb 20, 2024, at 9:22 PM, Zeng, Yi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I wanted to ask if there is a way to save each frame of a volume morph through the command line, or if a feature like this could be added? I would like to use each frame of the volume morph series (as .mrc) to export into an external program, but the only way I've found at the moment is to manually change each frame in the morph slider then save that frame. It doesn't appear there is the same coordset slider functionality of the volume morph slider for atomic models, which would be really handy in my situation if the morph has lots of steps.
Many thanks Jack
I would think using the perframe command to save the map while the morph is played can easily save each in a separate file. Tom
On Feb 21, 2024, at 8:55 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Jack, My understanding is that unlike an atomic morph which is calculated as a trajectory (multiple coordinate sets), the intermediates of a volume morph are not all saved in memory at the same time because each one can be quite large. So there isn't a single command that could save them all at the same time.
However, you may be able to use the "volume morph" command to do the same thing you are now doing manually, by including the "playRange" option to halt the morph at a particular stage, then using "save" to save a map, then using "volume morph" again with a different "playRange" [... etc. ...] It may be rather tedious but possibly better than moving the slider by hand. See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
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 Feb 20, 2024, at 9:22 PM, Zeng, Yi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I wanted to ask if there is a way to save each frame of a volume morph through the command line, or if a feature like this could be added? I would like to use each frame of the volume morph series (as .mrc) to export into an external program, but the only way I've found at the moment is to manually change each frame in the morph slider then save that frame. It doesn't appear there is the same coordset slider functionality of the volume morph slider for atomic models, which would be really handy in my situation if the morph has lots of steps.
Many thanks Jack
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Hi Tom and Elaine, Thanks for both suggestions. Using perframe following volume morph did the trick: volume morph #1,2 playStep 0.016666 frames 60; perframe "save '~/Desktop/tmp/$1.mrc' #3" frames 60 format %3d
participants (3)
-
Elaine Meng -
Tom Goddard -
y.zeng＠victorchang.edu.au