Is there an output directory command for spin movies or morphs?
Hi, I've given my students an assignment due on Monday which includes making a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put? Thanks, Ralph
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
Hi Ralph, I don't know of a solution to change the behavior of the icon (maybe one of the programmers can suggest something), but I see in the documentation https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home
... that it runs a command like:
movie record; turn y 2 180; wait; movie encode ~/Desktop/movieN.mp4
(all on one line with multiple command separated by semicolons, where N is automatically incremented so that you can save multiple files instead overwriting).
Thus one possibility is instead of clicking the icon, to issue that same set of 3 commands, again all in one line separated by semicolons, except change the output movie pathname "~/Desktop/movieN.mp4" to a different pathname. It should be a folder location that exists, and filename ending in ".mp4" ... also the whole pathname would need to be enclosed in quotation marks if it contains spaces. Maybe that is too difficult, but the only solution as a nonprogrammer that I can think of at this time.
Sorry for the inconvenience.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2022, at 5:47 AM, Ralph Loring via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I've given my students an assignment due on Monday which includes making a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put? Thanks, Ralph
Hi Elaine, Great! That works! I can't easily get to my desktop on my office computer unless I go to OneDrive, but it works if I point to the Videos folder instead. I was trying to do that, but didn't know about the semicolons. Thanks so much!! Now if I can just generalize this as directions for the students without knowing much about their directory structures... Ralph Loring
On Thu, Feb 3, 2022 at 2:18 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Ralph, I don't know of a solution to change the behavior of the icon (maybe one of the programmers can suggest something), but I see in the documentation https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home
... that it runs a command like:
movie record; turn y 2 180; wait; movie encode ~/Desktop/movieN.mp4
(all on one line with multiple command separated by semicolons, where N is automatically incremented so that you can save multiple files instead overwriting).
Thus one possibility is instead of clicking the icon, to issue that same set of 3 commands, again all in one line separated by semicolons, except change the output movie pathname "~/Desktop/movieN.mp4" to a different pathname. It should be a folder location that exists, and filename ending in ".mp4" ... also the whole pathname would need to be enclosed in quotation marks if it contains spaces. Maybe that is too difficult, but the only solution as a nonprogrammer that I can think of at this time.
Sorry for the inconvenience.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2022, at 5:47 AM, Ralph Loring via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi, I've given my students an assignment due on Monday which includes making
a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put?
Thanks, Ralph
Hi Ralph,
The problem is that Microsoft OneDrive has decided to move your Desktop folder so ChimeraX cannot find it.
So you get "Output directory does not exist" for C:/Users/r.loring/Desktop when you try to save your movie. I am not sure what you used to save that movie because it is doing a rock command and ChimeraX does not have any button to save a rocking movie, so you must have opened a script that explicitly listed that non-existent directory.
Then it appears you tried the Snapshot toolbar button which tries to save an image on the desktop and it gave "Permission denied writing file: C:/Users/Public/Desktop/image1.png". That is because Chimera asked to save to "~/Desktop" and somehow OneDrive has made that turn into C:/Users/Public/Desktop which you are not allowed to write files to.
Then you proceeded to try to save to various other directories that don't exist. From what I read online about OneDrive, if it is synchronizing your desktop icons to the cloud (which you can turn off) it will move your personal desktop to C:/Users/r.loring/OneDrive/Desktop. But I see from the commands you tested that gave an error that the folder does not exist. Then you tried "C:/Users/r.loring/OneDrive - Northeastern University/Desktop". Maybe that would have worked by you would have to use quotation marks in the ChimeraX command because it has spaces in the path.
In short ChimeraX would have to have special code to figure out where OneDrive has put your Desktop directory to get the toolbar snapshot and "spin movie" icons to be able to write their output file. It doesn't have that. Searching online I was not able to find out how in Python you can figure out what OneDrive has done with your Desktop folder. If I do figure it out some day I can fix ChimeraX to use that. Here is the bug report from 9 months ago where I tried to figure out this OneDrive problem, but so far no solution.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4567
If anyone knows the Python magic to find the Desktop directory location even when OneDrive moves it somewhere, tell me and I can use that in ChimeraX.
Tom
On Feb 3, 2022, at 2:26 PM, Ralph Loring via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, Great! That works! I can't easily get to my desktop on my office computer unless I go to OneDrive, but it works if I point to the Videos folder instead. I was trying to do that, but didn't know about the semicolons. Thanks so much!! Now if I can just generalize this as directions for the students without knowing much about their directory structures... Ralph Loring
On Thu, Feb 3, 2022 at 2:18 PM Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote: Hi Ralph, I don't know of a solution to change the behavior of the icon (maybe one of the programmers can suggest something), but I see in the documentation <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home>
... that it runs a command like:
movie record; turn y 2 180; wait; movie encode ~/Desktop/movieN.mp4
(all on one line with multiple command separated by semicolons, where N is automatically incremented so that you can save multiple files instead overwriting).
Thus one possibility is instead of clicking the icon, to issue that same set of 3 commands, again all in one line separated by semicolons, except change the output movie pathname "~/Desktop/movieN.mp4" to a different pathname. It should be a folder location that exists, and filename ending in ".mp4" ... also the whole pathname would need to be enclosed in quotation marks if it contains spaces. Maybe that is too difficult, but the only solution as a nonprogrammer that I can think of at this time.
Sorry for the inconvenience.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2022, at 5:47 AM, Ralph Loring via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi, I've given my students an assignment due on Monday which includes making a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put? Thanks, Ralph
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participants (3)
-
Elaine Meng -
Ralph Loring -
Tom Goddard