Re: [Jmol-users] Jmol 12.0.RC19 released

[Robert H. <ha...@st...>]

oh, yeah! Make that 18!

On Fri, Jun 11, 2010 at 7:49 AM, Nicolas Vervelle <nve...@gm...>wrote:

> Wasn't it RC18 ?
>
> Nico
>
> On Fri, Jun 11, 2010 at 2:35 PM, Robert Hanson <ha...@st...> 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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>>
>>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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