Hi Christian, I have fixed this problem in tonight's ChimeraX daily builds. Details are in ChimeraX bug report https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7491 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7491> 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. Tom
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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