Thanks, Egon. Friends, this release represents several major advances for
Jmol.
Still could be some issues, of course, but here we go.....
JmolData.jar
This is a slimmed down version of Jmol.jar that we are experimenting with.
It's hot off the griddle as we say in Minnesota -- I just put the finishing
touches on it this morning. It's a command-line-only operation, designed for
extracting data from a model or set of models and, oddly enough, has
ABSOLUTELY NO VISUALIZATION CAPABILITY. I know -- sounds ridiculous -- and
maybe it is, but with JmolData and some clever scripting you can get just
about any information you want out of a model -- whether it be an XYZ file,
CIF crystal struture, or PDB biomolecule -- and output it any way you want.
I realize it's pushing the limit of what a "molecular visualization
application" is all about, but I suggest it will find many uses. Typical
command line operation would look like this:
java -Xmx512m -jar "JmolData.jar" -pj "script xxx.spt" yourfile.cif
or
java -Xmx512m -jar "JmolData.jar" -ps "xxx.spt" myfile.xyz
-j means "execute this script after reading the file"
-s means "execute script in this file"
-p means "output only the results of the PRINT command"
There are several more options such as -d debug, -J excute script BEFORE
reading the file or loading the script file in the case of -s.
You are limited to commands that don't have to do with visualization --
there are bonds but no "sticks", atoms but no "dots", helices but no
"cartoons". I'd be very interested to hear from people whether this just
duplicates what is available elsewhere or actually might be useful.
helix(resNo, "infoType") function
This function is specifically for proteins and demonstrates the amazing
capability of quaternions to simplify structure analysis. It takes two
parameters -- a residue number such as 1, 2, 3, or if there are multiple
chains, an atom expression such as {helix} or {10-30} or {*.ca} that can be
used to get a residue. (Only the first is used), and a word in quotes:
"point" the point on the local helix axis closest
to the "quaternionFrame" reference atom (CA, C, or N)
for the given residue
"axis" the local helix axis for this residue
"radius" the vector from the "point" to the reference atom
"angle" the angle of rotation from this point to the next in the helix
"draw" the draw command that will draw the axis vector
"array" an array containing the point, axis, and radius vectors
While I realize that only a select few officianados will be interested in
this, a neat application of it is the next command:
select {*}
quaternion difference draw
See http://chemapps.stolaf.edu/jmol/docs/examples-11/qhelix/qhelix.htm -- my
first published Jmol WebExport!
This command draws the set of helical axes for all residues in the set and
perhaps indicates what quaternions have to do with this. A quaternion
expresses a frame of reference. A quaternion difference describes the axis
and angle necessary to take one frame to another. So, that "axis" n and
"angle" theta you get from the helix() function is actually the axis and
angle associated with a quaternion dq:
dq = {cos(theta/2), sin(theta/2)*n}
where n is the unit vector along the axis, axis/|axis|.
dq is simply q_i+1 / q_i - the "right difference" in this quaternion
algebra. (Or is it "left"?) Anyway, the calculation is extremely simple, and
the result works for both helices and sheets.
VRML exporter
I've improved the quality of the VRML exporter for atoms, bonds, cartoons,
and isosurfaces. Try it for yourself. Here's an example:
http://chemapps.stolaf.edu/jmol/docs/misc/1crn.vrml (might have to work on
the default perspective there!)
Bob
> --
> Post-doc @ Uppsala University
> http://chem-bla-ics.blogspot.com/
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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