I was hasty in posting my question, because within the hour I rediscovered
how I had done this in Chime, and it works fine in Jmol.
My script syntax is: select protein; select *A; color atoms blue; select
*B; color atoms red; (or whatever colors you wish).
However, I now have a different problem. I wanted to use this technique in
showing the different segments of hemoglobin, but the pdb file for this compound
appears to be too large for Jmol to handle. It loads in Chime, but does not
display in Jmol. Is there a size limit on the structures Jmol will handle?
I had noted earlier that the very large protein ricin failed to load as well.
When displaying structures composed of two or more peptide chains, e.g.
insulin, the chains may be given different colors by the color chain
command. In both Chime and Jmol the colors are designated by default. Is
it possible to assign other colors to the chains? I have not found a
Rasmol command that permits this to be done.
There is no direct way to assign different colors to the chains ... but
there is a workaround.
Jmol uses different colors and a different algorithm from RasMol/Chime.
RasMol/Chime starts with the same color, regardless of what the chain
Jmol always uses the same color for the same chain identifier. And the
Jmol colors are shades of pastels.
The workaround is as follows:
You can select sets of atoms and color them however you want. So you can say
select :a; color atoms salmon
select :b; color atoms orchid
select :c; color atoms lightSkyBlue
Take these script commands and put them in a file called
´myChainColors.txt´. You can then say
Whenever you want to apply these colors.
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