Dear all,
I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it.
I am using the following command (e.g.) to "create" the morph:
volume morph #1,2 frames 50
After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution.
I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version.
Any help would be greatly appreciated.
Best wishes,
Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden
Hi Karim, Yes the morph is added as a new model. The command both creates the morph and plays it. However, the default is only 25 frames (playstep 0.04 frames 25) and may finish playing very quickly, so maybe you didn’t notice it. For example, commands
open emdb:1283 open emdb:1284 volume morph #1,2
…create #3 as the morph and quickly show it. Could try more frames if you want it to take longer:
close #3; vol all show volume morph #1,2 playstep 0.01 frames 100
See description of command options: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2020, at 10:06 AM, Karim Rafie karim.rafie@umu.se wrote:
Dear all, I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it. I am using the following command (e.g.) to "create" the morph:
volume morph #1,2 frames 50
After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution.
I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version. Any help would be greatly appreciated. Best wishes, Karim
Hi Elaine,
Thanks a ton. I'll give it a go ASAP.
Best, Karim
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________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, January 28, 2020 7:28:14 PM To: Karim Rafie karim.rafie@umu.se Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] volume morph
Hi Karim, Yes the morph is added as a new model. The command both creates the morph and plays it. However, the default is only 25 frames (playstep 0.04 frames 25) and may finish playing very quickly, so maybe you didn’t notice it. For example, commands
open emdb:1283 open emdb:1284 volume morph #1,2
…create #3 as the morph and quickly show it. Could try more frames if you want it to take longer:
close #3; vol all show volume morph #1,2 playstep 0.01 frames 100
See description of command options: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2020, at 10:06 AM, Karim Rafie karim.rafie@umu.se wrote:
Dear all, I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it. I am using the following command (e.g.) to "create" the morph:
volume morph #1,2 frames 50
After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution.
I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version. Any help would be greatly appreciated. Best wishes, Karim
Would be nice if the volume morph showed a slider so you could move through the morph. I'll add a feature request for that.
But you can replay the morph you created by adding the "model" option to the morph command, for example,
volume morph #1,2 model #3
which avoids creating a new morph which would happen if you rerun your command without the model option.
Tom
On Jan 28, 2020, at 10:33 AM, Karim Rafie karim.rafie@umu.se wrote:
Hi Elaine,
Thanks a ton. I'll give it a go ASAP.
Best, Karim
Get Outlook for Android https://aka.ms/ghei36 From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, January 28, 2020 7:28:14 PM To: Karim Rafie karim.rafie@umu.se Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] volume morph
Hi Karim, Yes the morph is added as a new model. The command both creates the morph and plays it. However, the default is only 25 frames (playstep 0.04 frames 25) and may finish playing very quickly, so maybe you didn’t notice it. For example, commands
open emdb:1283 open emdb:1284 volume morph #1,2
…create #3 as the morph and quickly show it. Could try more frames if you want it to take longer:
close #3; vol all show volume morph #1,2 playstep 0.01 frames 100
See description of command options: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph>
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2020, at 10:06 AM, Karim Rafie karim.rafie@umu.se wrote:
Dear all, I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it. I am using the following command (e.g.) to "create" the morph:
volume morph #1,2 frames 50
After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution.
I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version. Any help would be greatly appreciated. Best wishes, Karim
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, yes that'd be great. Thanks for pointing out how to review the movie frames.
Best, Karim
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________________________________ From: Tom Goddard goddard@sonic.net Sent: Tuesday, January 28, 2020 8:14:28 PM To: Karim Rafie karim.rafie@umu.se Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] volume morph
Would be nice if the volume morph showed a slider so you could move through the morph. I'll add a feature request for that.
But you can replay the morph you created by adding the "model" option to the morph command, for example,
volume morph #1,2 model #3
which avoids creating a new morph which would happen if you rerun your command without the model option.
Tom
On Jan 28, 2020, at 10:33 AM, Karim Rafie <karim.rafie@umu.semailto:karim.rafie@umu.se> wrote:
Hi Elaine,
Thanks a ton. I'll give it a go ASAP.
Best, Karim
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 28, 2020 7:28:14 PM To: Karim Rafie <karim.rafie@umu.semailto:karim.rafie@umu.se> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] volume morph
Hi Karim, Yes the morph is added as a new model. The command both creates the morph and plays it. However, the default is only 25 frames (playstep 0.04 frames 25) and may finish playing very quickly, so maybe you didn’t notice it. For example, commands
open emdb:1283 open emdb:1284 volume morph #1,2
…create #3 as the morph and quickly show it. Could try more frames if you want it to take longer:
close #3; vol all show volume morph #1,2 playstep 0.01 frames 100
See description of command options: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2020, at 10:06 AM, Karim Rafie <karim.rafie@umu.semailto:karim.rafie@umu.se> wrote:
Dear all, I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it. I am using the following command (e.g.) to "create" the morph:
volume morph #1,2 frames 50
After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution.
I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version. Any help would be greatly appreciated. Best wishes, Karim
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Karim Rafie -
Tom Goddard