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

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

---

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