Useful chimera commands

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.