Thanks for the response to my message. I've been tied up with something and now it's quite late in Europe so I'll just send a brief reply to a couple of points and any further info later.
1. My interest is only in proteins where the hydrogens have been added. The database of the proteins I wish to display is predominantly the Richardson 500, where the resolution is never more than 2 angstroms, all the hydrogens have been added, and ambiguous residues checked manually. We are only interested in displaying H- bonds we are pretty sure about. 2. Our database is of hydrogen-bonded small 3D protein motifs, and includes all the H-bonds in the proteins. These have been derived using Janet Thornton's HBPlus program. However this is not public domain. The program program from the student many years ago is first rate. It was initially written by a lecturer in computing science here in Glasgow and the student made modifications. This was the brightest PhD student my colleague ever had. I don't think there is any question about the quality of the program. The suggestion of writing extra scripts seems unattractive at first sight. At the moment, after a search I am allowing a user to fire up Jmol showing the motifs in the context of the protein all generated on the fly. It's tricky enough to generate javascript controls for a particular situation in the context of the pdb file and the residues in the motifs. I haven't done anything with Jmol for two years (my web app uses 10.2) so perhaps I am overestimating the difficulty of the problem. David PS The web application I am using can be found at http:// motif.gla.ac.uk/motif/index.html. To see what I mean: ->Motifs in a Protein ->eg 1BX4 and Asx Turn ->3D ->Single Motif Display ->Motif 1 ->Hydrogen Bonds on (nothing happens) I would like to display the H-bond from Asn to main-chain NH. If you choose Beta Turn for the same protein, the main-chain - main- chain H-bonds can be displayed. _______________________________________________________________ Dr. David P. Leader, Faculty of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 (0)141 330 5905 http://doolittle.ibls.gla.ac.uk/leader The University of Glasgow, charity number SC004401 _______________________________________________________________ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
