Re: [chimerax-users] saving multiple .obj files from a morph
On Jun 9, 2021, at 3:38 AM, Brett Murrah murrahx5@att.net wrote:
I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this:
perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10
PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can.
Thanks you for any help! Brett
Hi Brett, I'm guessing you meant to send this to chimerax-users@cgl.ucsf.edu (CC'd here, the recommended address for questions).
The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small?
You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX:
perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe
https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html
The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up):
perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe
... but that gave an "incomplete quoted text" error which I will report as a bug. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Minor update: further tests suggest that the all-on-one line approach will work if a space is inserted between the second quotation mark and the first semicolon.
Elaine
On Jun 9, 2021, at 8:02 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
On Jun 9, 2021, at 3:38 AM, Brett Murrah murrahx5@att.net wrote:
I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this:
perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10
PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can.
Thanks you for any help! Brett
Hi Brett, I'm guessing you meant to send this to chimerax-users@cgl.ucsf.edu (CC'd here, the recommended address for questions).
The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small?
You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX:
perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe
https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html
The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up):
perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe
... but that gave an "incomplete quoted text" error which I will report as a bug. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
I this is working!!! Thank you.
Sent from my iPhone
On Jun 9, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Minor update: further tests suggest that the all-on-one line approach will work if a space is inserted between the second quotation mark and the first semicolon.
Elaine
On Jun 9, 2021, at 8:02 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
On Jun 9, 2021, at 3:38 AM, Brett Murrah murrahx5@att.net wrote:
I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this:
perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10
PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can.
Thanks you for any help! Brett
Hi Brett, I'm guessing you meant to send this to chimerax-users@cgl.ucsf.edu (CC'd here, the recommended address for questions).
The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small?
You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX:
perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe
https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html
The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up):
perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe
... but that gave an "incomplete quoted text" error which I will report as a bug. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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Elaine Meng