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

[Christian Tüting]

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 <chimerax-users at cgl.ucsf.edu>
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

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