I think I can help you except for one part. In short you want the
'spectrum' command. For example, you can color a chain R, based on the
b-factor with the command:
spectrum b, green_yellow, chain R
The problem is that you must color based on a numeric value that each
atom has associated. So let's say you want to color a helix from
residue index 300-400. I tried:
spectrum resi, green_yellow, resi 300-400
spectrum resi_number, green_yellow, resi 300-400
...and several other variations without success. Somebody out there
might no the answer to this problem.
-Charlie
Peter Teriete wrote:
Dear All,
I'm trying to color a protein cartoon structure from N- to C-terminal
with a green to yellow gradient. Had a browse around and couldn't quite
find the correct command. Any pointers are welcomed.
Peter
