On 2005-08-05 (12:46) David Leader wrote: >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 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?". >
you could use solid (or dashed) monitor lines, but you would have to build the script yourself. this requires that you know the atom numbers of the hydrogen bond donors and acceptors: monitor atomno1 atomno2 but the command syntax is (obviously) very simple. I'll be happy to help out with some kind of routine, if possible given you rdata structure. if you are interested, feel free to email me off list. regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:raleigh "I sometimes go to my own little world, but that's okay, they know me there." - Joel Hodgson ------------------------------------------------------- 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
