First of all --oops! (three counts)
1) I didn't intend to forward a gif -- this is NOT from Jmol!!!
(though I think Jmol could to at least as good a job on that)
2) I incorrectly described how to insert variable data (free-form
lists of values) into an ISOSURFACE command in Jmol 11.1.18.
Use the VARIABLE keyword.
3) I forgot to mention that ANY regular atom property (temperature, charge,
atomIndex, etc.) can also be mapped.
Here it the full message again, revised:
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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.
2) Select those atoms:
select 1.2 # only the second model in the first file
3) Read the file data into a variable:
myData = load("data.txt")
4) Create a data set based on that variable. Note that the
prefix "property_" is REQUIRED. This is what tells Jmol to
convert the data to floating point values rather than just
keep it as a string, and to assign the values to individual atoms.
DATA "property_whatever @myData"
5) Now you can, for instance, use this as part of the atom label:
select 1.1; label "%a %4.2{property_whatever}"
(That would be 4 characters right-justified with 2 decimal places.)
6) For an isosurface, just use either of these commands to map those
numbers onto the solvent surface:
ISOSURFACE saSurface map property_whatever
or
ISOSURFACE saSurface map VARIABLE myData
The subtle difference here is that with using property_whatever, you
have the ability to assign some specific subset of the atoms the values
you want. In the VARIABLE case, we are assuming that all the data -- at least
any point up to where we are interested in ALL files loaded is represented.
This is because in the VARIABLE case we have not done any mapping of specific
values to specific selected atoms the way we have using the data set.
To color the van der Waals surface, use:
ISOSURFACE VDW 100% saSurface map property_whatever
I thought that this might be a nice default, so you can even just do the
following:
isosurface property_whatever
or for a slightly smoother rendition:
ISOSURFACE VDW 100% molecular map property_whatever
If all you are interested in is a quick-and-dirty mapping, and your data
are for all the atoms in the model, then all you need is:
x = load("data.txt")
isosurface variable x
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Bob Hanson
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