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
To save images in nogui mode, you need to start up ChimeraX with the --offscreen flag. However, that code isn't working right now, so I've filed a bug report on your behalf.
-- Greg
On 11/7/18 8:07 AM, Lukas Pravda wrote:
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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I have fixed the bug where opening a map in ChimeraX in nogui mode raises an error. It was trying to show the volume viewer gui interface. This does not fix the problem that offscreen rendering is not working in nogui mode noted in this bug report
https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1427 https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1427
Tom
On Nov 7, 2018, at 10:09 AM, Greg Couch gregc@cgl.ucsf.edu wrote:
To save images in nogui mode, you need to start up ChimeraX with the --offscreen flag. However, that code isn't working right now, so I've filed a bug report on your behalf.
-- GregOn 11/7/18 8:07 AM, Lukas Pravda wrote:
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
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 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
participants (3)
-
Greg Couch -
Lukas Pravda -
Tom Goddard