[Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions

Enrico Martinez jmsstarlight at gmail.com
Fri Jan 14 14:17:42 PST 2022

Dear Chimera's users!
First I wish Happy New Year to everyone!
I am just switching from Chimera to ChimeraX that I am going to use in
no-gui (batch) mode to prepare screen shots of protein-ligand
interactions based on the protein-ligand docking poses. Basically I am
loading a pdb file of the complex (consisted of protein and ligand in
multi-model format) from the terminal of my macOSX. I have a template
for a batch file created in the bash script on the fly, that I used 2
years ago with an early version of ChimeraX.

# a batch file for chimeraX
printf "open ${pdb}
view; zoom 1.0; turn x 90; turn z -80;
# options for appearance
preset 'overall look' publication
# set bg powder blue
set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02

# make info of the screen
2dlab create title text \"${pdb_name}\" color red font gothic xpos .04
ypos .92 size 35

# options for light
light depthcuestart .4 depthcueend .8; lighting full intensity 1.4
shadows true qualityOfShadows finer

save image ${structure}/${pdb_name}.png format png width 800 height
600 supersample 4 transparentBackground false
exit" > chimeraX.${pdb_name}.cxc"

then I use it directly in terminal as
chimerax-daily chimeraX.${pdb_name}.cxc"

may you suggest some commands that I may introduce into my batch file to
1) delete all models from the multi-model pdb file with the exemption
of the first model.
2) switch from cartoon to surface representation of the protein
3) visualize protein-ligand non-covalent interactions in the current model

Yours with thanks

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