Hello, Thanks a lot for the awesome tool ! I have a question about how to use some commands that are not yet included in the python API : for instance "measure volume". I can run it using a cxc with : */usr/bin/chimerax --script measure.cxc --nogui --exit* Where *measure.cxc *contains looks like : *open test.mrc volume #1 level 0.42 measure volume #1* I don't understand how to do the same with a python script. Is there some way to use chimerax.tools(measure area/volume) to get this tool to work from within a python script ? My use case is that I am running this measurement for different thresholds, and I would like those thresholds to depend on the value of previous thresholds, hence I need looping. For now, I am calling subprocess on the .cxc command above from a python script, but this means that I need to load the mrc every time... Thanks in advance for your help ! Best, Vincent
Hi Vincent, We're glad you like ChimeraX! Without resorting to python, you can do some looping by embedding your current commands in a perframe command. The level value in your volume command would be the $1 variable to gradually change in the loop. See perframe description and examples to see if it can do what you want (may take some experimentation, I usually have a few rounds of trial and error with this kind of thing myself): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 21, 2023, at 1:52 AM, Vincent Mallet via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Thanks a lot for the awesome tool !
I have a question about how to use some commands that are not yet included in the python API : for instance "measure volume". I can run it using a cxc with : /usr/bin/chimerax --script measure.cxc --nogui --exit Where measure.cxc contains looks like : open test.mrc volume #1 level 0.42 measure volume #1
I don't understand how to do the same with a python script. Is there some way to use chimerax.tools(measure area/volume) to get this tool to work from within a python script ?
My use case is that I am running this measurement for different thresholds, and I would like those thresholds to depend on the value of previous thresholds, hence I need looping. For now, I am calling subprocess on the .cxc command above from a python script, but this means that I need to load the mrc every time...
Thanks in advance for your help !
Best, Vincent
Vincent, I think this can also be done in Python, in case you prefer that. In the Python API, there's a `run` function for running commands. For a lot of commands, this function will return a relevant value. For example: from chimerax.core.commands import run vol = run(session, "measure volume #1") `session` is defined by default as the current ChimeraX session. `vol` is the total enclosed volume of #1. Best, Tony On Fri, Jul 21, 2023 at 9:38 AM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Vincent, We're glad you like ChimeraX!
Without resorting to python, you can do some looping by embedding your current commands in a perframe command. The level value in your volume command would be the $1 variable to gradually change in the loop. See perframe description and examples to see if it can do what you want (may take some experimentation, I usually have a few rounds of trial and error with this kind of thing myself):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 21, 2023, at 1:52 AM, Vincent Mallet via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Thanks a lot for the awesome tool !
I have a question about how to use some commands that are not yet included in the python API : for instance "measure volume". I can run it using a cxc with : /usr/bin/chimerax --script measure.cxc --nogui --exit Where measure.cxc contains looks like : open test.mrc volume #1 level 0.42 measure volume #1
I don't understand how to do the same with a python script. Is there some way to use chimerax.tools(measure area/volume) to get this tool to work from within a python script ?
My use case is that I am running this measurement for different thresholds, and I would like those thresholds to depend on the value of previous thresholds, hence I need looping. For now, I am calling subprocess on the .cxc command above from a python script, but this means that I need to load the mrc every time...
Thanks in advance for your help !
Best, Vincent
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thanks so much for this prompt responses, it has helped me a lot ! On Fri, Jul 21, 2023 at 6:04 PM Tony Schaefer <tony.schaefer.chem@gmail.com> wrote:
Vincent,
I think this can also be done in Python, in case you prefer that. In the Python API, there's a `run` function for running commands. For a lot of commands, this function will return a relevant value. For example:
from chimerax.core.commands import run vol = run(session, "measure volume #1")
`session` is defined by default as the current ChimeraX session. `vol` is the total enclosed volume of #1.
Best,
Tony
On Fri, Jul 21, 2023 at 9:38 AM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Vincent, We're glad you like ChimeraX!
Without resorting to python, you can do some looping by embedding your current commands in a perframe command. The level value in your volume command would be the $1 variable to gradually change in the loop. See perframe description and examples to see if it can do what you want (may take some experimentation, I usually have a few rounds of trial and error with this kind of thing myself):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 21, 2023, at 1:52 AM, Vincent Mallet via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Thanks a lot for the awesome tool !
I have a question about how to use some commands that are not yet included in the python API : for instance "measure volume". I can run it using a cxc with : /usr/bin/chimerax --script measure.cxc --nogui --exit Where measure.cxc contains looks like : open test.mrc volume #1 level 0.42 measure volume #1
I don't understand how to do the same with a python script. Is there some way to use chimerax.tools(measure area/volume) to get this tool to work from within a python script ?
My use case is that I am running this measurement for different thresholds, and I would like those thresholds to depend on the value of previous thresholds, hence I need looping. For now, I am calling subprocess on the .cxc command above from a python script, but this means that I need to load the mrc every time...
Thanks in advance for your help !
Best, Vincent
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
Tony Schaefer -
Vincent Mallet