Wasn't it RC18 ?
Nico
On Fri, Jun 11, 2010 at 2:35 PM, Robert Hanson <[email protected]> wrote:
> 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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