> For our teaching application it is important to differentiate clearly
> between, say, "trace" and "ribbons" when the two renderings are overalyed
> on a single molecule.
[snip]
> spacefill off;
> wireframe off;
> trace on;
> color green;
This should say 'color trace green'
> ribbons on;
> color red;
This should say 'color ribbons red'
When you say 'color blue' you are really saying 'color atoms blue'. The
color of the trace/ribbon/etc. changes because it is inheriting the color
of the alpha carbon.
I strongly recommend that people always explicitly say
'color {object} COLOR-SPECIFICATION'
And never use the shortened version.
Note that Jmol offers many more options than RasMol/Chime regarding
independent coloring of trace/ribbons/etc. Therefore, scripts that take
advantage of these features may not be backwards compatible.
Miguel
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