ChimeraX normally does not update volume surfaces until they are drawn. The volume is normally drawn after each command you type so this is not a problem. But when you run a series of commands with the --cmd start-up option there is no drawing. A similar situation is when you open a ChimeraX command script file (.cxc suffix). ChimeraX handles script files specially and the volume surface updates immediately without waiting to redraw. I've changed the --cmd option so it runs the commands as if they are a script file.

On Aug 17, 2022, at 3:54 AM, Christian Tüting via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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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