[Chimera-users] Visualisation in Headless Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 28 09:31:50 PDT 2019

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.

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.

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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