Useful chimera commands
Revision as of 03:06, 24 March 2020 by TBalius
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 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: