[Chimera-users] Visualisation in Headless Chimera

James Starlight jmsstarlight at gmail.com
Thu Mar 28 04:11:18 PDT 2019

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

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!


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