Re: [chimerax-users] Measure volume at multiple threshold levels not function

Dear Elaine, yes, this is also somehow my explanation. The update is done after execution of the single line multi-command. So in my gui example, running the command volume #1 level 2; measure volume #1 twice, first gives the values of the "old" level, and in the 2nd time, the updated values. So the command must be fully executed, which is the reason, that the cxc script file works, i guess. Best Christian

...

...

Elaine Meng 08/17/22 4:48 PM >>> Dear Christian, Our "volume expert" is away this week, but my best guess is that it has something to do with when the isosurface is updated. It may not get updated (especially in a nogui situation) when the commands are joined within a single line with semicolons. Best, Elaine

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 17, 2022, at 4:05 AM, Christian Tüting via ChimeraX-users wrote:

Dear all,

I found a dirty workaround for my case.

I have the commands in a list and execute them like this: chimerax --nogui --cmd '{";".join(commands)}' --exit

And this is not functional.

But writing the commands to a cxc file, and executing this, will give the correct values:

with open("tmp.cxc", "w") as f: f.write("\n".join(commands))

chimerax --nogui tmp.cxc --exit

So somehow the newline after level change is important?!

Best Christian

...

...

...

Christian Tüting via ChimeraX-users 08/17/22 12:57 PM >>> Dear ChimeraX-Team,

I have an issue with the volume measure tool. I would like to measure the volume at different thresholds. Using the gui mode, I can type the following:

volume #1 level 1 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06

volume #1 level 2 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 2.144e+06

So this is functional in principle. But I would like to run this in no gui mode, so the commands are ";" seperated.

But, even in gui mode, I got the following:

(threshold was set to 1 before executing)

volume #1 level 1; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06

volume #1 level 2; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06

So the threshold level is not applied, prior to the measurement of the volume.

And this is the same in the no-gui mode. I would like to check the volume at 5 different levels, but I got always the same value when executing:

"/usr/libexec/UCSF-ChimeraX-daily/bin/ChimeraX --nogui --cmd 'open cryosparc_P42_J241_002_volume_map_sharp.mrc; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1' --exit"

Is there any command, that the threshold level is somehow applied, and the measure volume is executed correctly?

The problem is present in UCSF ChimeraX version: 1.4.dev202202240543 and UCSF ChimeraX version: 1.5.dev202207221833

Best Christian

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

_______________________________________________ ChimeraX-users mailing list Chim