It would be great to have these hydrogen-bond capabilities in Jmol. -Steve ````````````````````````````````````````````````````````` Steven B. Vik Department of Biological Sciences Southern Methodist University Dallas, TX 75275-0376 236 Dedman Life Sciences Bldg. Phone (214) 768-4228, Fax (214) 768-3955 E-mail [email protected], WWW http://faculty.smu.edu/svik ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> From: "[email protected]" > <[email protected]> > Reply-To: <[email protected]> > Date: Mon, 4 Oct 2010 17:14:09 +0000 > To: <[email protected]> > Subject: Jmol-users Digest, Vol 53, Issue 3 > > Date: Mon, 4 Oct 2010 08:40:25 -0500 > From: Robert Hanson <[email protected]> > Subject: Re: [Jmol-users] Jmol and DSSP > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > An interesting observation -- > > RasMol uses a "DSSP" method of calculating double bonds without actually > doing the DSSP calculation. What that does is -- it seems to me -- > improperly assign hydrogen bonds. If you read the DSSP paper carefully, you > see that although the same calculation is presented there for hydrogen bond > detection as used in RasMol (well, ALMOST the same...) the intent is to > define sheet and helix structure, not to correctly identify all hydrogen > bonds. Kabsch and Sander were purposely and explicitly generous in their > assignments. > > It seems to me a smarter idea would be to use the DSSP algorithm to select > only the defining hydrogen bonds that are used to identify helix, turn, and > bridge positions. > > Also, for the record, RasMol does not identify inter-chain hydrogen bonds, > which is also a bug, as far as I can tell -- or at least a misreading of the > DSSP paper. > > Here's a comparison: > > Rasmol: http://stolaf.edu/people/hansonr/jmol/1gua-rasmol.png > Jmol (with DSSP): http://stolaf.edu/people/hansonr/jmol/1gua-jmol.png > > The bonds in the Jmol version are colored by type (antiparallel white and > parallel cyan) > > Comments? > > Bob ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
