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<p class="MsoNormal">Hi Tom,<o:p></o:p></p>
<p class="MsoNormal">That worked perfectly. Thanks for the tip, and I’ll be sure to grab the new build.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Joel<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Tom Goddard <goddard@sonic.net><br>
<b>Date: </b>Tuesday, April 7, 2020 at 2:23 PM<br>
<b>To: </b>Joel Meyerson <jrm2008@med.cornell.edu><br>
<b>Cc: </b>"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>[EXTERNAL] Re: [chimerax-users] cxc script does not execute 'surface dust' command<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Joel, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> 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.<o:p></o:p></p>
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<p class="MsoNormal">Tom<o:p></o:p></p>
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<p class="MsoNormal">On Apr 7, 2020, at 10:37 AM, Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.5pt">Hi Joel,</span> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.5pt"> 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:</span><o:p></o:p></p>
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<p class="MsoNormal">close all<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">open map.mrc<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">turn x 90<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">volume erase #1 center 175,160,314 radius 100 outside true<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">volume #2 calculateSurface true<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">surface dust #2 size 40<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal">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.<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><a href="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=">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#calculateSurfaces</a><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"> Tom<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal">On Apr 7, 2020, at 7:09 AM, Joel Meyerson <<a href="mailto:jrm2008@med.cornell.edu">jrm2008@med.cornell.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi,<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">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.<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Do you know why the command is not working inside a script?<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">close all<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">open map.mrc<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">turn x 90<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">volume erase #1 center 175,160,314 radius 100 outside true<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">surface dust #2 size 40<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Thanks for the help.<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Joel<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
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