At 6/13/12, Jane Richardson wrote: > For the Rama plots, do you know who wrote the script for that > in JMol and might be able to make a couple of changes that would > improve it enormously? At present, it's nearly useless because the > -180 to +180 range is compressed into the center, there are no > numbers on the axes, and when you click on a point you get its > residue name and number but not the phi,psi values. It would be > good, altho not essential, to show contours for the favored and > outlier divisions; we'd be glad to provide those either for > current MolProbity general-case or for the new version that will be > adopted soon for PDB use. Also, the documentation for the Rama > feature (as well as the whole Ramachandran plot page, before I > fixed it) always refers to "psi,phi". It's not just non-standard > to reverse the sequence order, it's actually wrong, because a > psi,phi plot is occasionally used and looks very different, since > it shows psi(i-1), phi(i) rather than the real Rama plot which is > phi(i), psi(i).
Dear Jane, The code within Jmol for Jmol's built-in Ramachandran capability was probably written by Bob Hanson -- [email protected] -- he is the primary developer of Jmol. I am copying this to jmol-users, where most of the issues in Jmol are discussed and then remedied by Bob. -Eric ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
