This will probably be the last set of innovations for a while -- time to
get back to teaching...
11.3.14 will fix a few bugs and introduce some valuable functionality in
the area of color schemes. It was a rather complicated set of
modification; testing appreciated!
-- you can map color schemes with customized ranges onto atoms, labels,
etc. with the COLOR command.
select *;
color atoms property partialcharge "rwb" range -0.5 0.5
-- you can define your own color schemes by name, and you can redefine
any Jmol color scheme such as "roygb" if you really want to. This means,
for example, that you could redefine the atom colors 1-120 as a color
scheme and then call that up for atoms or any other reason, using the
elemno property for the coloring.
select none; color "myscheme=[xFF0000] [xFFFF00] [x00FF00] [x00FFFF]
[x0000FF]"
select none; color "roygb=[xFF0000] [xFFFF00] [x00FF00] [x00FFFF] [x0000FF]"
select none; color "roygb=" # un-define the scheme roygb
select *;
color atoms property elemno "myscheme" range 1 100
-- you can remap isosurfaces with difference coloring schemes after the
fact.
isosurface s1 molecular map mep
color $s1 "rwb" range -0.3 0.3
color $s1 "bwr"
Enjoy!
Bob
# bug fix: HDO not recognized as "water"
# bug fix: rotateSelected MOLECULAR not around {0 0 0}
# bug fix: -g ignored on -n option, even if -w is present
# bug fix: unknown color palette could cause error
# new feature: %l atomic element number
# new feature: APPLICATION -q (quality) option
# new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent
[n]|opaque] [colors...]
# adjustment: setting JPG default quality to 75, not 100
# new feature: {r,g,b} can be used in place of [r,g,b] for indicating
color,
# allowing programmatic color definition:
#
# r = 255; g = 255; b = 0;
# background [EMAIL PROTECTED],@g,@b}
# new feature: expanded color command for properties
#
# color atoms property partialcharge "rwb" range -1.0 1.0
#
# and reverse with range inverted:
#
# color atoms property partialcharge "rwb" range 1.0 -1.0
# new feature: unlimited user-defined color schemes:
#
# select none;
# color "myname=[xff00ff] [xffff00] [xff00ff]"
#
# colors must be [xRRGGBB] format for this one
# new feature: fully remappable isosurface using COLOR command:
#
# isosurface s1 molecular map mep
# color $s1 "bwr"
# color $s1 "rwb" range -0.2 0.2
--
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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