cxc script does not execute 'surface dust' command
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
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#calculateS... Tom
On Apr 7, 2020, at 7:09 AM, Joel Meyerson <jrm2008@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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@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#calculateS... <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#calculateS...>
Tom
On Apr 7, 2020, at 7:09 AM, Joel Meyerson <jrm2008@med.cornell.edu <mailto:jrm2008@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@sonic.net> Date: Tuesday, April 7, 2020 at 2:23 PM To: Joel Meyerson <jrm2008@med.cornell.edu> Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@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@sonic.net<mailto:goddard@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@med.cornell.edu<mailto:jrm2008@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=K3OasPvfEwCSBQF7d93l6bxyjgtwrxI5zVAWQU5l8w0&s=ULjryel4n0mCj0gMPvLq92wttrzwKXIrPM2tAiNJgoM&e=> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Joel Meyerson -
Tom Goddard