> I appreciate that Jmol (like Rasmol) allows one to turn HBonds on and > off (and make them stretch to the backbone or stop in mid-air) but > the decision about what is a hydrogen bond is made by the program > apparently.
The rules for treating hbonds are like the rules for treating covalent bonds ... If hbond information is in the file then Jmol will respect that information. Otherwise, Jmol will attempt to determine hbonds. Be advised that the hbonds constructed by Jmol are only backbone hbonds constructed using simple algorithms. If someone wanted to have a student do some work in this area ... > The data that I am displaying in my web pages is of small > hydrogen-bonded motifs in proteins, where the whole point is that > there are hydrogen bonds other than those that the program may regard > as standard. Indeed the motifs are so defined by the scientific > expert for whom I am putting the site together. Each motif has its > own rules for which atoms should be joined by Hbonds, so my question > is "are there any commands I can use to make Jmol display dotted > lines between the atoms I specify following these rules?". If you are willing to put your files in PDB format you can use the CONECT record type to specify your hbonds. Jmol will use the hbonds from the file and will not construct its own. (I doubt if this has been used/tested very much, so let me know if you find any bugs) There are currently no commands to construct hbonds or covalent bonds. We can talk about that if you want ... Miguel ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
