[chimerax-users] cxc script does not execute 'surface dust' command

[Tom Goddard]

Hi Joel,

  The trouble is ChimeraX does not recompute map surfaces until they are displayed, and during a script they are not displayed.  Adding the command "volume #2 calculateSurface true" will fix it:

close all
open map.mrc
turn x 90
volume erase #1 center 175,160,314 radius 100 outside true
volume #2 calculateSurface true
surface dust #2 size 40

This is really cryptic.  I'll see if I can make ChimeraX calculate the volume surfaces immediately when it is running in a script.  The calculateSurfaces option is described in the documentation but you would never know to look for it.

	https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#calculateSurfaces

  Tom


> On Apr 7, 2020, at 7:09 AM, Joel Meyerson <jrm2008 at med.cornell.edu> wrote:
> 
> Hi,
> I am observing inconsistent behavior in the ‘surface dust’ command. When I launch ChimeraX and execute the following commands one-by-one at the command line everything works as expected. However, if I place the commands in a cxc script, then double click the script ChimeraX launches and the script executes, but the ‘surface dust’ command does not hide the dust. In addition, within that same session I can then enter the ‘surface dust’ command manually and it works as expected. I’m running ChimeraX Daily 0.93 (2020-04-04) on Mac OS 10.15.1.
>  
> Do you know why the command is not working inside a script?
>  
> close all
> open map.mrc
> turn x 90
> volume erase #1 center 175,160,314 radius 100 outside true
> surface dust #2 size 40
>  
> Thanks for the help.
> Joel
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