Thanks, Nico, for releasing 11.1.18. Fast on its tail is 11.1.19:
Jmol 11.1.19 introduces the ability to let users add any amount of
numerical atom-based properties to a model (as in 11.1.18) and now
COMPARE them using SELECT, DISPLAY, etc.:
x = load("mydata.dat"); data "property_myprop @x"
...
select model = 3 and property_myprop < 1e-5;
x = {carbon}[5].property_test
x = {carbon}.property_test.min
x = {carbon}.property_test.max
Of course, you can display this information in labels:
label "%a data=%{property_myprop}"
and you can list it all for a set of atoms using a variable:
x = {1-10}.label("%a %{property_myprop}")
message @x
IN ADDITION (this is the best part!) you can now color atoms, stars,
shapes, whatever, using these properties. It will take some time to work
out the details, but basically, we have six property color "schemes"
(same as for isosurfaces):
rwb red-white-blue
bwr blue-white-red
roygb red-orange-yellow-green-blue
bgyor blue-green-yellow-orange-red
low red-orange-yellow
high yellow-green-blue
[of course, it shouldn't be too hard to now include designer color
schemes, but we aren't quite there yet]
1. So first you pick a property color scheme:
propertyColorScheme = "bgyor" # reverse of the default
2. Next you simply color based on a property:
color atoms property surfacedistance
No kidding!
3. Or, if you want to create your own set of atom properties, just load
the numbers into a variable and color based on that:
x = load("myparam.dat")
color cartoons translucent variable x
4. If you are only interested in a small set of the atoms and don't want
to have to include data for all of them, just use the data command and
apply the color using a property_xxxx data set built from a variable:
x = load("molecule1.dat")
select molecule=1
data "property_molecule1 @x"
color atoms property_molecule1 #note the underscore
In this way you can target just the atoms for which you want to set the
color. Note that the RANGE of color is based on the atoms selected when
the data set is loaded. It may be a different set of atoms that are
colored -- that's fine. Totally up to you.
More examples:
propertyColorScheme = "rwb"
select *
color atoms property temperature
propertyColorScheme = "roygb"
x = {*:1}.temperature.all # a new item selector, like .min and
.max, but the full list
select *
color atoms variable x
x = load("mydata.txt")
select molecule=1
data "property_whatever @x"
color atoms property_whatever
Fun!
Bob
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