ps -- references at that bottom are to an alternative method of
visualization: We have incorporated into Jmol the "promolecular NCI" --
Noncovalent interactions -- calculation published recently in JACS[1] and
JCTC[2] by the Yang group at Duke. (The results of SCF NCIPLOT output are
also visualizable in Jmol using the isosurface command, but the CONTACT
command can be used as a simple way to check out and compare the NCI result
at least qualitatively.) But that's another story.
On Wed, Jun 22, 2011 at 3:03 AM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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