Jmol users --
Not "big" as in lots of bytes, but BIG in terms of impact. I believe Erik
Wyatt (undergraduate at St. Olaf) and I have cracked the nonbonding
interations nut. With this announcement we hereby introduce what I just
checked in as Jmol 12.1.51_dev: the CONTACT command. This new command
displays objects that float in space between two interacting atoms. These
could be hydrophobic interactions or hydrogen bonds or in principle any
other interactions. A set of "teasers" can be found at
http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm
The objects created are similar to isosurfaces (and, in fact, are derived
from them) and are created very efficiently and quickly. They can be
rendered as flat planes perpendicular to the line connecting the interacting
atoms, as cigar-shaped connections along those lines, and as volume-rendered
dots. There are several adjustable parameters that allow fine-tuning the
visualization to different sizes and contacts. They can be isolated very
specifically to any set of atoms, and it appears so far to us that the
presence of absence of hydrogen atoms does not make much of a difference.
Thus, they can be implemented for any PDB, CIF, XYZ, or MOL files. All you
need are some atoms.
I predict these will be a big hit. These few examples will have to suffice
for now.
One question: Is anyone aware of anything like this in PyMOL or VMD or other
packages?
The CONTACT command is not at all limited to biomolecules, and I am hoping
some people will give it a try with totally nonbiological systems.
Just to give you a hint as to how they are created, it involves another new
capability in Jmol 12.1.51: the ability to design any combination of two VDW
surfaces based on any combining formula you can write into a Jmol math
expression. As such, these objects were relatively easy to implement. Also
important was a third new capability -- the capability to cleanly trim any
mapped isosurface based on a range of values, including volume-rendered
points. This is all now possible with the ISOSURFACE command and carried out
using a much simplified syntax with the CONTACT command. For starters all
you need to do is identify a ligand and enter:
contact {ligand}
Then go from there. See
Jmol.properties<http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/Jmol.properties?revision=15632&content-type=text%2Fplain>for
details.
The CONTACT command will be in 12.1.51, which I hope we can release later
this week. We do have a few more touches to add to this still. Looking to
publish this by the end of the summer. For a possible figure in the paper
and an acknowledgment, get your examples in early! We're very interested to
see what people can do with these and what we need to do to make them
especially useful.
- Bob
[1]
* "Revealing Noncovalent Interactions",
* Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia
Contreras-Garcia, Aron J. Cohen, and Weitao Yang,
* J. Am. Chem. Soc., 2010, 132, 6498-6506. email to
[email protected]
[2]
*
* "NCIPLOT: A Program for Plotting Noncovalent Interaction Regions"
* Julia Contreras-García, Erin R. Johnson, Shahar Keinan, Robin Chaudret,
Jean-Philip Piquemal, David N. Beratan, and Weitao Yang,
* J. of Chemical Theory and Computation, 2011, 7, 625-632
--
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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