The 2009 Gordon Research Conference on Visualization in Science and
Education is over. It was unbelievably cool. It's strict policy not to
discuss anything that was at that meeting, so please don't ask me to do
that. However, some ideas were transmitted to me during the meeting from
Jmol users, and I did have a few hours to work on Jmol here and there
outside of the actual conference hours, so there are a few new features in
Jmol 11.8.RC4 even though I try not to do that with a "release candidate."
Three new features and one crazy idea of note:
Mouse-movable labels
Lone pairs and radicals
CIF data in structured form
Mouse-movable labels
Using
set Picking Label
which generally turns labels on and off when an atom is clicked now also
allows fast movement of a label using the mouse. Just hold SHIFT down while
picking the atom associated with an already-displayed label. Dragging the
mouse then drags the ("SHIFTS" the) label position around.
Lone pairs and radicals
--
Thank Mike Abraham for reminding me that we've wanted lone pairs for SOME
TIME (like forever). Now you have them. It occurred to me that really they
are cartoonish more than real, and if you think about it, the LcaoCartoon
objects are positionable exactly the way we would want to position lone
pairs. So now you can position a lone pair any way you would a lobe. Just
use LONEPAIR instead of CREATE:
select oxygen
lcaoCartoon color red
lcaoCartoon LONEPAIR "sp2a"
lcaoCartoon LONEPAIR "sp2b"
The default is 0.5 Angstroms from the associated atom center, which
basically places it directly in the center of an LCAO orbital. But you can
place the electrons wherever you want:
lcaoCartoon scale 1.5 LONEPAIR "sp2b"
The actual size of the dots or distance between the dots is not adjustable.
(The current setting was chosen by an august consultant panel.) The scale
factor just moves them along the axis. While considering that, it seemed
simple enough to do single electrons, so we also have:
lcaoCartoon RADICAL "pza"
which, of course, places a single dot along that axis.
CIF data in structured form
---
Recently I added a method of getting PDB header data directly into a
variable. This is now expanded to CIF files and renamed "fileInfo". It's
obtainable via the getProperty() function. Realize that the file is read a
second time to do this -- it isn't stored by default -- but once it is read
the second time, it is then saved. This could be an issue with very large
files.
load 1crn.pdb
print getProperty("fileInfo","HELIX")
H1 ILE A7 PRO A 19 13/10 CONFORMATION RES 17,19 13
H2 GLU A 23 THR A 30 1DISTORTED 3/10 AT RES 30 8
load 1mng.cif
print getProperty("fileInfo","models",0,"_audit_author.name")
Lah, M.S.
Dixon, M.
Pattridge, K.A.
Stallings, W.C.
Fee, J.A.
Ludwig, M.L.
Note that for _loop data, the individual "columns" of data become an array:
load quartz.cif
x = getProperty("fileinfo","models",0,"_atom_site_label")
show x
x = ["Si", "O"]
Thanks go to Brian McMahon for that suggestion.
The crazy idea is really crazy. It's to extend Jmol to display N-dimensional
data as 3-dimensional projections. This is important in some fields, but not
at all trivial. We have the know-how in my collaborator Andy Hanson, of
Indiana University. This can be done relatively simply, I think, but we'll
see. Mostly it's a matter of porting Andy's C++ code over to Java and then
figuring out how to patch that into Jmol. I'll start a new branch for it
when we get going on it and see how it goes.
All for now,
Bob (enroute to Berlin)
--
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
nday, February 5, 1900
--
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