FYI Congrats to Bob and the others!
---------- Forwarded message ---------- From: Robert Hanson <hans...@stolaf.edu> Date: Fri, Jun 11, 2010 at 2:35 PM Subject: [Jmol-users] Jmol 12.0.RC19 released To: jmol-us...@lists.sourceforge.net 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 ------------------------------------------------------------------------------ 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 jmol-us...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ 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 _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss