On 11/17/2010 08:42 PM, Andreas Prlic wrote:
> Ok here my suggestion for a palette that resolves to various
> distinguishable shades of blue and yellow for color blind people and
> still looks kind of ok-ish for all others (thanks to
> http://colorschemedesigner.com/ for making this selection easy )
>
> Primary Color:
> 104BA9 284A7E 052D6E 447BD4 6A93D4
> Secondary Color A:
> AA00A2 7F207B 6E0069 D435CD D460CF
> Secondary Color B:
> C9F600 9FB82E 83A000 D8FA3F E1FA71
> Complementary Color:
> FFA200 BF8B30 A66A00 FFBA40 FFCC73
>
> For having good contrasts for "color chain" it would be good to rotate
> column by column from left to right through this grid...
>
I wrote a Jmol function "color_by_chain(atom-object type)" (see below)
that implements Andreas color scheme for chains. Just put the script
into a file and load it. (It will need Jmol version 12.x. I tested it
with version 12.0.22.)
Afterwards you can color the current selection by calling this command.
If you provide an empty "atom-object type" all object types like
cartoon, trace are colored alike (more precise: set to none, meaning
they inherit it from "atom"). If you name an object type only this type
is colored.
Examples:
color_by_chain("cartoon");
color_by_chain("");
The colors are not tied to a specific chain id like in the standard
chain color scheme. Instead they are assigned alphabetically to the
present chain ids (e.g. A,B,C in structure 1 will be colored like G,I,Y
in structure 2, if there are no other chains).
Unfortunately Jmol 12.0.22 doesn't like it if you try to provide the
object type by a variable (type="cartoon"; color @type red) and throws
an error. So I had to add each type individually and also couldn't use a
loop for the "empty object type" case.
Regards,
Rolf
==========================================================
function color_by_chain(type) {
var chain_list = script("show chain").trim().lines;
var chain_count = chain_list.length;
define current_selection selected;
var color_list =
array("x104BA9","xAA00A2","xC9F600","xFFA200","x284A7E","x7F207B","x9FB82E","xBF8B30","x052D6E","x6E0069","x83A000","xA66A00","x447BD4","xD435CD","xD8FA3F","xFFBA40","x6A93D4","xD460CF","xE1FA71","xFFCC73");
var color_count = color_list.length;
for (var chain_number=1; chain_number<=chain_count; chain_number++) {
var color_index = chain_number % color_count;
var chain_color = color_list[color_index];
var selection_expression = "current_selection and :" +
chain_list[chain_number];
select @selection_expression;
if (type == "") {
color atom [...@chain_color];
color backbone none;
color cartoon none;
color dots none;
color halo none;
color label none;
color meshribbon none;
color polyhedra none;
color rocket none;
color star none;
color strand none;
color strut none;
color trace none;
}
if (type == "atom") {
color atom [...@chain_color];
}
if (type == "backbone") {
color backbone [...@chain_color];
}
if (type == "cartoon") {
color cartoon [...@chain_color];
}
if (type == "dots") {
color dots [...@chain_color];
}
if (type == "halo") {
color halo [...@chain_color];
}
if (type == "label") {
color label [...@chain_color];
}
if (type == "meshribbon") {
color meshribbon [...@chain_color];
}
if (type == "polyhedra") {
color polyhedra [...@chain_color];
}
if (type == "rocket") {
color rocket [...@chain_color];
}
if (type == "star") {
color star [...@chain_color];
}
if (type == "strand") {
color strand [...@chain_color];
}
if (type == "strut") {
color strut [...@chain_color];
}
if (type == "trace") {
color trace [...@chain_color];
}
}
select current_selection;
}
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