Thank you, Nico, for releasing 12.0.RC19. I know the idea of a "release
candidate" is that we prefer not to have new features, but not in this case.
Jmol 12.0 will have some radically new capability, and 12.0.RC19 has that.
If I ever can slow down a bit, I will document all this, but for now I have
to just give you a teaser:
set modelKitMode
This mode allows rapid "prototyping" of small molecules -- build them up
from methane, drag atoms to new places, drag atoms with minimization (this
is REALLY fun!) to change conformations or stereochemical configurations.
Closest thing to "Chime Sculpt" we'll ever see, but WAY more fun. Create
molecules and save them as MOL files. Use CTRL-Z and CRTL-Y to undo/redo
your changes.
select search("...SMARTS string...")
SMARTS is a language designed to search molecular structures for
two-dimensional connectivity. Jmol now has a full implementation of SMARTS
and adds a few special extensions. For example:
select search("{C}C=O") # alpha carbons
select search("{[CH,CH2]}C=O") # alpha carbons with hydrogens
select search("C{[H]}=CC(=O)[C,O]") # beta hydrogens of alpha-beta
unsaturated ketones or esters
Traditional SMARTS is only designed to FIND patterns; the added {...} here
also allows us to SELECT specific atoms within that pattern. This is the
powerful part.
bioSMARTS
Jmol extends SMARTS to cross-linked protein and nucleic acid sequence/base
pair sequence searching. Want to find all the CG basepairs ?
select search("~C:G")
just like that!
How about a CAG hybridized run?
select search("~CAG:CTG")
(The colon crosses over to the other strand.)
To make sure this is really not just a cross-over of two RNA pieces, we use
the SMARTS ring notation, with colon to indicate basepair.
select search("~C:1AG:CTG:1")
(Note -- prior to using ":" you need to calculate hbonds.)
SMILES and bioSMILES generation.
Jmol 12.0 will generate SMILES strings and bioSMILES (which combines ALL
patterns in the model, whether biomolecular or not) for any model or subset
of a model.
It's as easy as
print {*}.find("SMILES") // standard SMILES
print {*}.find("SMILES",true) // bioSMILES
A description of Jmol 3D-SMILES and bioSMILES can be found at
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/smiles/package.html
reading SMILES to 3D
As if that were not enough, the Jmol application and signed applet can read
SMILES strings into 3D coordinates. This is a bit in flux, because it
requires a server at Indiana University, but it's pretty good. Ring
conformations are a bit odd. To do this, just use "$" at the beginning of
the "file name" in a load command:
load "$CCCC" # butane
One nice thing is that the AS keyword lets you save that on your hard drive:
load "$C/C=C\\C" AS "cis-butene.mol"
Note that we need \\ there because we are working with strings, where \x
means something special. "\\" is an "escaped" backslash.
I hope people will experiment with these and provide suggestions. There's
more there that I haven't mentioned. The full list of new features and bug
fixes is at
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/Jmol.properties
The demo pages and documentation haven't caught up yet, so this is all you
get for now.
Let's get some cool summer projects going!
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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