Re: [Jmol-users] Ramachandran issues in Jmol
Dear Jane, That would be me! Thanks for your feedback on this. I've actually been meaning to talk with you for a long time, just not gotten around to it What version of Jmol are you using? -- When you click on a point on the 3D Ramachandran plot you should see three numbers: phi, psi, and what I will call omega', and when you hover over a point you should see those as well. Earlier versions of Jmol behaved as you describe, and I agree those are not very helpful. omega' is the difference between omega and +/-180, which ever is closer to zero. (I don't know a simple way of saying that.) The reason we use omega', is that, unlike traditional Ramachandran plots, we have that third dimension. It makes no sense to use omega itself, because values close to ideal such as 179 and -179 would be in totally different places. The way we do it, the Z axis can be read as difference from ideal and cis-prolines show up as outliers, which is convenient. I would love to show contours. It might be a trick to do that in 3D, but maybe not too bad. I think I could manage it. If you send me the coordinates of the contours, I'll look into that. The Ramachandran plot is interesting, of course, but also note that you have full access to the phi, psi, and omega values themselves for any specific residue or group of residues for any sort of analysis or tabulation you would like. Note also that there is a subtle distinction between helix and within(helix) in case you start being interested in comparing Ramachandran angles between structures. within(helix) cuts out the first and last residue of each helix structure. Aside from that, not sure you know that Jmol can now read and display Kinemage files created by MolProbity. Also, while I'm at it -- are you aware the MolProbity reverses the placement of the hydrogen atoms on CH2 groups when it calculates H atoms? Probably not something anyone but me cares about. But that's one of the things I've been meaning to talk with you about. Bob Hanson On Wed, Jun 13, 2012 at 8:22 PM, Eric Martz ema...@microbio.umass.eduwrote: 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 -- hans...@stolaf.edu -- 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 -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Ramachandran issues in Jmol
Dear Jane, I just found out that we (Proteopedia's SAT) is the responsible for Jmol displaying element information instead of the default phi,psi and omega values on a Ramachandran plot. Please hover points on http://proteopedia.org/wiki/index.php/User:Jaime_Prilusky/Ramachandran_plot for a correct behavior. Sorry for the confusion. I will try to fix this ASAP. Jaim On Jun 14, 2012, at 7:14 PM, Robert Hanson wrote: Dear Jane, That would be me! Thanks for your feedback on this. I've actually been meaning to talk with you for a long time, just not gotten around to it What version of Jmol are you using? -- When you click on a point on the 3D Ramachandran plot you should see three numbers: phi, psi, and what I will call omega', and when you hover over a point you should see those as well. Earlier versions of Jmol behaved as you describe, and I agree those are not very helpful. omega' is the difference between omega and +/-180, which ever is closer to zero. (I don't know a simple way of saying that.) The reason we use omega', is that, unlike traditional Ramachandran plots, we have that third dimension. It makes no sense to use omega itself, because values close to ideal such as 179 and -179 would be in totally different places. The way we do it, the Z axis can be read as difference from ideal and cis-prolines show up as outliers, which is convenient. I would love to show contours. It might be a trick to do that in 3D, but maybe not too bad. I think I could manage it. If you send me the coordinates of the contours, I'll look into that. The Ramachandran plot is interesting, of course, but also note that you have full access to the phi, psi, and omega values themselves for any specific residue or group of residues for any sort of analysis or tabulation you would like. Note also that there is a subtle distinction between helix and within(helix) in case you start being interested in comparing Ramachandran angles between structures. within(helix) cuts out the first and last residue of each helix structure. Aside from that, not sure you know that Jmol can now read and display Kinemage files created by MolProbity. Also, while I'm at it -- are you aware the MolProbity reverses the placement of the hydrogen atoms on CH2 groups when it calculates H atoms? Probably not something anyone but me cares about. But that's one of the things I've been meaning to talk with you about. Bob Hanson On Wed, Jun 13, 2012 at 8:22 PM, Eric Martz ema...@microbio.umass.edumailto:ema...@microbio.umass.edu wrote: 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 -- hans...@stolaf.edumailto:hans...@stolaf.edu -- 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 -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- 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 Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security
[Jmol-users] Ramachandran issues in Jmol
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 -- hans...@stolaf.edu -- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
