Just checked in -- a new idea for color schemes.
The idea here is to allow a special form of color scheme that can be
used to replace the standard Jmol/Rasmol colors for elements and
residues. I think this addition goes a long way toward that.
# new feature: byElement and byResidue color schemes allow
# customized element and residue coloring schemes.
# built-in include: byElement_Jmol, byElement_Rasmol,
# byResidue_Jmol (shapely) and byResidue_Rasmol (amino)
# with abbreviations byElement == byElementJmol; byResidue == byResidue_Jmol
#
# for example:
#
# color atoms "byresidue_Jmol"
#
# Users can set up their own byElement and byResidue color schemes
# simply by preficing a name with "byElement" or "byResidue":
#
# color "byElement_Mine=[x......] [x......] [x......] ..."
# 0(unknown) 1(H) 2(He) ...
#
# then:
#
# color atoms "byElement_Mine"
#
# RANGE min and max are ignored for byElement and byResidue schemes,
# and there is no scaling done ever, so effectively these prefixes
# make the correlated value a simple index into the array.
# This is what one would want for something that should be a given
# for a specific element or residue
#
# Residue indexes in order correspond to the groupID of an atom:
#
# 0 noGroup,
# 1 ALA, ARG, ASN, ASP, CYS,
# 6 GLN, GLU, GLY, HIS, ILE,
# 11 LEU, LYS, MET, PHE, PRO,
# 16 SER, THR, TRP, TYR, VAL,
# 21 ASX, GLX, UNK,
# 24 A, +A, G, +G, I, +I,
# 30 C, +C, T, +T, U, +U
#
# so this opens the door to user-created residue coloring schemes.
#
# color "byResidue_Mine=[x......] [x......]..."
# nogroup ALA ...
#
# then
#
# color cartoons "byResidue_Mine"
In connection with this, you can now
show colorscheme byElement_jmol
show colorscheme byElement_rasmol
show colorscheme byResidue_jmol
show colorscheme byResidue_rasmol
in order to see exactly what colors Jmol is using and adapt them as you
like.
For example:
x = script("show colorscheme byResidue_jmol").split(" = ")[0]
Now x is a list of the color codes Jmol uses for the "color shapely"
scheme.
and
c_ala = x.split(" ")[2]
c_arg = x.split(" ")[3]
etc. gets you each individual color.
Possibly useful.....
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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