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

[Tom Goddard]

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 at 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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