[Chimera-users] Visualisation in Headless Chimera

James Starlight jmsstarlight at gmail.com
Thu Mar 28 09:49:26 PDT 2019

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
#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
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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