hi,
thought I would followup this thread with some feedback, having tried
to implement various flavors of this recently.
################
1. coloring based on a built-in property works well and is very cool:
y = {*}.occupancy.all
data "property_charge @y"
propertyColorScheme = "bwr"
color atoms property_charge
one caveat: the name of your new property must begin with
"property_". this was not clear to me initially, and I spent a while
wondering why "my_charges" kept failing. :-)
note: propertyColorScheme is also very useful and easy to implement.
################
2. coloring based on values in an external data file was cumbersome
when using any subset of atoms in a structure:
y = load("charge.dat")
data "property_charge @y"
propertyColorScheme = "bwr"
color atoms property_charge
I could not easily align the values in my data file with the atom
count in the selected set in Jmol; the atom count was always
different, which threw off the coloring scheme. in the end, I put the
values in the occupancy column of the pdb file and used method 1,
which worked great.
a suggestion: use a more explicit atomno:value syntax in the data
file, and have Jmol ignore values for atoms that are not in the
selected set.
kudos for great work,
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I: M-1 im: molvisions
Washington St., Blacksburg, VA 24061
04-16-07. We will not forget you.
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