Useful chimera commands

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Command line

You might like to make a small molecules (eg. HEM) part of the surface of the protein instead of separate:

 surfcat one #1:1-290
 surf one probeRadius 1.4

You might want to color by partial charge:

 rangecolor charge,a min red 0 white max blue sel
 rangecolor charge,a -1.0 red 0.0 white 1.0 blue sel

This command will color the selected atoms by there charge.

Example Command-line script to save an image

open ../poses_clust_int.mol2
open ../rec.crg.pdb
surface #1
 color orange #1:.B
 color byhet,a #1:.B
 focus #0
 transp 80,s #1
 sop cap off
 set bg_color white
 unset depthCue
 set silhouette
set bg_color white
unset depthCue
set silhouette
focus #0
turn y 160
 turn x 20
display #0.1
copy file ./C648_1.png png width 3840.0  height 1941.0 supersample 1
# this copy command will save the image, give the full path where you want to save the image
# you may want to ajust the width and height. 

Here are some tutorials: