Bob and all:
In 1991-92, I was just getting into molecular modeling while on sabbatical at
UNC Chapel Hill. While there I got to know Fred Brooks in the computer science
department. He had obtained manipulator arms from one of the National Labs
(used to operate from the outside of a closed environment) and connected them
up to a state of the art (in 1991) SGI workstation. He had a screen which was
about 4' x 6' on which he could project a protein and a substrate, and using
3-D glasses you could see the whole complex in 3-D. You could now use the
manipulator arms to "drive" the substrate into the active site, manipulating
both substrate and protein. Furthermore, an on-the-fly force field calculation
fed back the interaction energies to your hands so you could feel when you were
"bumping" into something. It was great fun!!!
He also had the "pixel plane machine" -- one processor per pixel. Great
animation capability:-)
Phil
On May 28, 2010, at 10:22 AM, Robert Hanson wrote:
> It's been a VERY good week. First we get a working model kit for Jmol, and
> now SMILES to 3D:
>
> From the application or SIGNED applet:
>
> load SMILES "CC1C(C)c...@h]coc(=O)C1"
>
> or, simply,
>
> load $CC1C(C)c...@h]coc(=O)C1
>
> ($ indicates SMILES, like = indicates PDB)
>
> and
>
> print load("$CCCC")
>
> or
>
> Var x = load("$CCCC")
>
>
> Need I say more? :)
>
> see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?USEDSIGNED
>
>
> Yes, I suppose I do need to say more.
>
> This uses a web service at Indiana University
> http://cheminfo.wikispaces.com/smi23d that appears to use PCMODEL for its
> converter. The idea is similar to the way "=xxxx" goes to the RCSB site.
>
> The implementation is not entirely reliable, at least I noticed that it did
> double-bond stereochemistry wrong for some simple conjugated systems. For
> example:
>
> F/C=C/C=C\C
>
> gives the expected E,Z configuration, but
>
> F/C=C/C=C/C
>
> ALSO gives that configuration.
>
> To get E,E you have to use
>
> F/C=C/\C=C/C
>
> But that's not a valid SMILES string, as far as I know.
>
> So something is amiss there. And certain atoms such as [Na] aren't
> recognized. Also, formal charge is not recognized, for example [C+] doesn't
> result in fewer H atoms.
>
> C60's SMILES string didn't work.
>
> So it's definitely not a perfect solution. But it's a start.
>
> We need to do more testing on this, of course.
>
> Bob
>
>
> --
> 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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J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
[email protected]
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