Not sure what the mechanism should be to try to resolve the differences ...
Compromises? :-)
undisputed inorganic atoms: are 'hot pink' in the RasMol scheme are essentially 'unassigned' in the RasMol scheme
I feel like all atoms should be assigned unique colors and as I said, I think in the cases of elements without *strong* preferences for colors, related elements should have related colors. For example, the noble gases or the lanthanides, IMHO should have different shades that make it easy to realize it's in that set. I'm not even sure that my coloring scheme is the best here.
important organic atoms: the RasMol/Chime folks feel *strongly* about H, C, N, O, P, & S there is existing courseware that makes use of these colors even the color shade is important there are shade differences + Phosphorus is very different see below *
Personally, I don't have strong shade preferences and even with Phosphorus, I was trying to reproduce colors I observed in textbooks--without an accurate #. Obviously I should also have examined RasMol's colors too.
A lighter shade for carbon is probably good--it opens up darker shades for other elements.
However, I'd like to be a bit careful with "gold" for sulfur--I really think gold, silver, copper, etc. should look like those metals. Considering how much shades sometimes vary based on printing technique, are particular shades critical?
metals/others: there are a couple of dozen others elements that were assigned colors in RasMol RasMol scheme has duplicates - I want to eliminate these there are a few cases of agreement (chlorine) most are quite different
I looked at your coloring page: http://jmol.sourceforge.net/colors/
Some of the "Open Babel" colors don't look quite right, but I'll take your word that the colors represented are what's in the table. (It's been a while :-)
I guess it boils down to this:
- elements which have a "known color" either in existing graphics or common knowledge
- elements which IMHO should be assigned systematically
So I'll list a few problems I see with the rasmol colors:
- silicon is an orange-ish color (#DAA520), but IMHO it should be a grey-ish to match a Si wafer
- nickel is a copper-ish color (#A52A2A in fact, identical to Cu), but IMHO it should be a grey/blue
- iron is an orange-ish color (#FFA500), but should be well, iron grey (maybe grey/red for rust?)
- boron shouldn't be a neon green -- I often see it as pink
I don't know the origin of the Li and Na colors -- are they used in protein graphics?
A few things OB should fix:
- Xx should be a hot pink -- clear to see the dummy atoms (either that, or a dark, dark grey as something that should be ignored)
- F should be a neon green or light blue (like WebLab) which it tends to get in graphics I see around here
- Some elements seem to have drastically different colors from WebLab, which I thought I used as a reference
So I guess my question is this. Besides the colors that RasMol insists on (i.e., H, C, N, O, P, & S), what other colors are common/important?
-Geoff
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