Tim, I think you will like how this works. The idea is to set up a
property (like temperature, but of your own definition) and then use it
in the command
color atoms property_x
To set up "property_x", you load the values into a variable and then use
the DATA command
to assign that variable to a property. "x" here is arbitrary:
x = load("myfile.dat")
select *
data "property_tim @x"
Make sure the data are a single column -- the second of what you show
below. Then just
color atoms [cartoons, trace, etc.] property_tim
The idea is that once you have assigned the property to the atoms with
the data statement, then
you can color them using it.
If you don't have data for all the atoms, just supply the necessary data
for the SELECED atoms.
So, for example, if you are only coloring the alpha carbons, you can do
that using
select *.CA
data "property_ca @x"
The color scheme will be roygb.
Bob
Timothy Driscoll wrote:
>hi,
>
>I have a set of charge values for atoms in a pdb file. I'd like to
>color the structure according to those charges, but I'm a bit
>confused how to do that. I have this, from an email in march 2007:
>
>
>
>>Jmol 11.1.18 will allow a broad range of customized colorings for
>>isosurfaces as well as new capabilities for labels. Basically you can
>>read in any number of sets of atom-based data (charges, distances
>>from a
>>given point, anything) and then you can display that either in a label
>>or as a coloration of an isosurface. It's very simple:
>>
>>1) In a file, construct a list of the numbers you want to associate
>>with
>>atoms. Just any list separated by lines or spaces or tabs -- any white
>>space is fine. Just numbers. It does not have to be for ALL the atoms,
>>just whatever ones you wish to SELECT.
>>
>>2.5 2e-3
>>-2.54 3 6
>>etc.
>>
>>
>
>
>I grasp how to load the external dataset into Jmol, but how do I
>associate a particular charge with the correct atom? for example:
>
>atomnum charge
>1 -0.33
>2 0.32
>3 0.55
>4 -0.55
>5 0
>
>
>
>
>thanks for any help,
>
>tim
>
>
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