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

[Christian Tüting]

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 <meng at cgl.ucsf.edu> 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
<chimerax-users at cgl.ucsf.edu> 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 <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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