give this a try:
var m=255
var rc=xmax
var gc=xmin+0.5*(xmax-xmin)
var bc=xmin
var rw=1.9*(xmax-xmin)
var gw=0.7*(xmax-xmin)
var bw=0.9*(xmax-xmin)
var r=(m-Math.max(0,Math.floor(m*(1-Math.abs(x-rc)/rw))))
var g=(m-Math.max(0,Math.floor(m*(1-Math.abs(x-gc)/gw))))
var b=(m-Math.max(0,Math.floor(m*(1-Math.abs(x-bc)/bw))))
c=hexof(256*256*256-((r*256+g)*256+b)-1)
It's what I used for
http://www.stolaf.edu/people/hansonr/js/ptable/ptable.htm
(select color by "atomic no")
I think it's pretty smooth.
Bob
Miguel wrote:
no; it really is more of a rainbow. see attached gif for an
example.
Hmmm ... sure looks pretty ugly to me
well, it is a useful way to trace the path of the backbone from N to C
visually. I can't comment on the colors themselves. ;-)
I found all the colors confusing.
I assume that the idea is to be able to look at a residue and judge where
it fits in the chain. With a broad palette of non-standard colors, how can
anyone possibly know what color comes first.
It *might* be better if the sequence was the colors of the rainbow ... but
it isn't.
So, that is why red->white->blue seemed better to me. The color spread is
simple and easy to interpret. I can look at a residue and know where it
fits relative to the chain length.
Q: What would be wrong with red -> white -> blue? It seems to me
that it would be much easier to visualize/interpret because there
would be less noise.
my only objection is that RWB might be confused with charge.
Agreed.
But since 'temperature' and 'charge' are already using red/white/blue I
thought that maybe it would be OK
would it be difficult to let the user define the start and end colors,
and have Jmol interpolate the colors between?
If you wanted to have a fixed number of colors (like 2 or 3) then it would
probably be pretty easy.
Having a variable number of colors might be more than I am willing to deal
with right now. But, if you catch me on a good day *after* the v10 release
I might reconsider.
Miguel
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Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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