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

[Joel Meyerson]

Hi Tom,
That worked perfectly. Thanks for the tip, and I’ll be sure to grab the new build.

Best,
Joel

From: Tom Goddard <goddard at sonic.net>
Date: Tuesday, April 7, 2020 at 2:23 PM
To: Joel Meyerson <jrm2008 at med.cornell.edu>
Cc: "chimerax-users at cgl.ucsf.edu" <chimerax-users at cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [chimerax-users] cxc script does not execute 'surface dust' command

Hi Joel,

  I changed ChimeraX so when it is executing a script it updates the volume surfaces immediately instead of waiting for graphics drawing.  So your original script will work in tonight's ChimeraX builds.

Tom


On Apr 7, 2020, at 10:37 AM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_docs_user_commands_volume.html-23calculateSurfaces&d=DwMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=K3OasPvfEwCSBQF7d93l6bxyjgtwrxI5zVAWQU5l8w0&s=wQnN1v0mKdYKSZpizKg_yzEgtOdtRli6FFbgJqNSrGc&e=>

  Tom



On Apr 7, 2020, at 7:09 AM, Joel Meyerson <jrm2008 at med.cornell.edu<mailto: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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