[Chimera-users] Visualisation in Headless Chimera

Greg Couch gregc at cgl.ucsf.edu
Thu Mar 28 13:40:06 PDT 2019

The software OpenGL library, libOSMesa.so, in Chimera is based on Mesa 
7.6.1.  Chances are that your system has a newer version available, so 
if you install it (eg., "sudo apt install libosmesas6" or "sudo yum 
install mesa-libOSMesa"), and remove the version in Chimera (might have 
to copy the system version to CHIMERA/lib, don't remember), it should be 
much better.

If that doesn't work, then I'd recommend getting the libOSMesa.so from 
ChimeraX and installing it in your Chimera library.  The one in ChimeraX 
is Mesa 18.2.5, and it uses llvm, unlike many of the system version of 
libOSMesa.so, so it supports newer OpenGL APIs. Ubuntu 19.04's 
libOSMesa.so is supposed to be the llvm version, but that isn't out yet.



On 3/28/19 9:49 AM, James Starlight wrote:
> Thank you so much, Elaine!
> Yes, indeed, I have tested it's a problem in set silhouettes command
> which cause headless-chimera to crush.
> the same is for the "preset" command.
> And the problem is on the step of the rendering of the image
> Rendering high resolution image...
> ./structure.sh : ligne 70 :  3515 Erreur de segmentation  (core
> dumped) chimera-batch ${pdb} ${temp}/chimera.${pdb_name}.com
> and here is my script
> set bgcol white
> set silhouette
> ~set depth
> ribscale licorice
> ribrep edged strand
> #light options
> light contrast 0.4
> light reflectivity 0.9
> #structure pre-processing
> ksdssp
> #use this commands to re-orient PDB
> turn x 90 center view
> #turn y 20 center view
> turn z -80 center view
> move z -15
> # make visualisation of b-factors
> rangecolor bfactor 2 blue 30 red 50 yellow
> # make a png immage
> copy file ./B-factors_EvXynTS_apo_340K.png png width 800 height 600
> Finally I just have checked it also in chimera-gui, everything works
> fine with the same commands!
> чт, 28 мар. 2019 г. в 17:31, Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi James,
>> (1) The black outlines are silhouettes, so if silhouettes cause the problem there is no way around it.  The preset also does some other things, however, so you could doublecheck just using the “set silhouettes” command instead of “preset.”
>> The image you attached is from the ribbon styles tutorial. The tutorial shows the commands you would need to make that image.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles.html>
>> Image description is "smooth ribbons, default lighting except decreased contrast and reflectivity”
>> …corresponding to the  the first two “set” commands in that tutorial (white background and black silhouettes) and the last two commands (lighting contrast and reflectivity).
>> (2) The “key” command option only enables interactive placement of a color key by hand using the GUI.  Sorry, there is no option to place the color key directly, without human intervention.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> On Mar 28, 2019, at 4:11 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>> Dear Chimera users!
>>> I am using headless version of Chimera inside of my Bash script to
>>> prepare images of the pdbs. Normally I provide a pdb file with a
>>> script in loop to obrain images automatically
>>> Here are some of my questions related to the visualisation:
>>> 1) I have a problem with the "preset apply publication 1"
>>> notably Chimera is crushed when I use #set silhouette option
>>> Is it possible to make "a black border of a selected thickness" for
>>> all of the elements of secondary structure of my proteins via some
>>> another command?
>>> Actually in terms of the cartoon's style (but not a colour) I would
>>> like to obtain something like was shown here
>>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles-contrast3-reflect5.png
>>> 2) I am using "rangecolor bfactor 2 blue 30 red 50 yellow" option to
>>> colour the structure according to the B-factor information provided in
>>> the given PDB.
>>> The problem is when I provide "key" option for it to place a colour
>>> diagram on the resulted picture I ontain a crush in headless version.
>>> Do some other methods exist for the placement of the colour legend for
>>> the B-factor colouring which could be used in the headless version?
>>> Thank you for help in avance!
>>> James
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