ChimeraX-users November 2018

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chimerax-users@cgl.ucsf.edu

4 participants
2 discussions

Incrementing value in perframe
by Scott, Brandon L. 09 Nov '18

09 Nov '18

I am attempting to use the measure convexity on each frame, and seem to have a mismatch between the frame number which goes from [0 - (N-1)] and the volume child which goes from [1 - N]. Is there a way to augment the $1 value to be $1+1? Attached are the command calls. This displays the convexity properly on the called frame: vseries play #1 jumpTo 1; measure convexity #1.2 smoothingIterations 12 palette cyan-gray-maroon range -1,1; The does not display it because of the mismatch: movie record; perframe "vseries play #1 jumpTo $1; measure convexity #1.$1 smoothingIterations 12 palette cyan-gray-maroon range -1,1;" range 1,200; wait 200; movie encode C:\Users\LLSM\Desktop\Convexity.mp4 quality highest framerate 25 Thanks in advance. -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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Render images in nogui mode
by Lukas Pravda 07 Nov '18

07 Nov '18

Hi all, I was wondering if there is a way how to generate images from linux terminal. I’ve come across a couple of very old posts in the mailing list stating that this was not possible at that time. So, I wonder if anything has changed. If I use cif files only, chimerax gives “Unable to render images to save them” message. If I try to include volumetric data from cryo-EM overlaid on the structure I get an exception during opening a *.map file. Please see the script below. The exception is in the attachment Best, Lukas open emd_8909.map volume #1 color white transparency 0.7 level 0.1 step 1 zoom 1.2 open 6ds5.cif set bgColor white hide selAtoms show selAtoms ribbons color bychain ribbons light full light shadow true save image default.png width 1600 height 1600 supersample 5 transparentBackground true turn y 90 save image y.png width 1600 height 1600 supersample 5 transparentBackground true turn z 90 save image z.png width 1600 height 1600 supersample 5 transparentBackground true

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