> 1) Is the secondary structure assignment function in 0.92 > more reliable? Or does the "WARNING: it will make mistakes, > so don't publish anything based on this algorithm!" statement > still apply?
Good question! I added that warning message to "util.ss" back when I believed that there was such as thing as "correct" secondary structure assignment and because util.ss had a very primitive H-bonding definition -- distance only. "dss" is something completely new. In creating the new "dss", I took some time to go through the 1983 DSSP paper (Kabsch & Sander) and discovered much to my surprise that the H-bond criterion used by DSSP has very little to do with what crystallographers today think about hydrogen bonds. Did you know that DSSP H-bonds can be as long as 5.2 Angstroms between heavy atoms (Fig 1)? Plus, there is no simple analytic form of their criterion provided which could be implemented by something like PyMOL. Furthermor, and more disturbing, I discovered that DSSP doesn't take backbone torsion geometry into account at all, which finally explained to me why so many DSSP-assigned PDB structures have obviously non-helical regions assigned as HELIX. It's just a naive algorithm, and as far as I'm concerned, H-bonds just aren't the whole story when it comes to secondary structure. Thus, I had to admit that DSSP itself wasn't correct with repect to my personal interpretation of secondary structure. In looking at RasMOL's code it suffers from some of the same problems, and I don't think it actually implements DSSP -- just an approximation to it. So I decided to create my own best-attempt at a secondary structure assignment algorithm based on the spirit of DSSP, but which also takes into account backbone geometry as well as hydrogen-bonding . Like DSSP, PyMOL's hydrogen-bonding criteria is angle-dependent, but the default range is more contemporary (within 3.2 A at 63 deg, 3.6 A at 0 deg). After validating the algorithm manually on ten structures, I sat down and visually compared PDB (DSSP) assignments to PyMOL's "dss" over several hundreds proteins. In general, both programs find the same set of helices and large sheets. However, they differ on the exact start and stop points of these elements. On small sheets or helices, one program may miss something that the other finds. However, divergent regions seemed to involve borderline cases for the most part. "dss" and DSSP seem to do equally well on cut-and-dry idealized systems. So "dss" is reasonably validated, in my view, but I am looking for feedback and specific problem cases when they're found. But speaking as an artist rather than as a scientist, I think "dss" has better aesthetics than DSSP when it comes to cartoon diagrams -- there are simply fewer goofy-looking assignments. Whether it is more scientifically correct or not is an open question. Cartoons themselves are pretty misleading...one might add. By the way, there are a some new settings in PyMOL 0.92 which cover h-bond detection and secondary structure assignment. Here are the most important ones: h_bond_max_angle, 63.0 h_bond_cutoff_center, 3.6 h_bond_cutoff_edge, 3.2 ss_helix_psi_target, -48.0 ss_helix_phi_target, -57.0 ss_strand_psi_target, 124.0 ss_strand_phi_target, -129.0 Basically, if helix or sheet hydrogen bonds are present, and backbone geometries are close to the target values, PyMOL will assign residues as helix or sheet. Otherwise, they're considered loops. The allowable Phi/Psi inclusion/exclusion boxes are adjustable with settings too. For the curious, my algorithm is about 1,000 lines of code and consists of the SelectorAssignSS function found in layer3/Selector.c around line 500. > 2) Is there a 0.92 function to calculate and map surface > potential? This would be useful beyond compare. I wish. Your choices for this are Grasp, MEAD, Delphi, or Zap. Only MEAD is freely available. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Neiditch, Matthew > Sent: Friday, October 31, 2003 12:46 PM > To: 'pymol-users@lists.sourceforge.net' > Subject: [PyMOL] secondary structure assignment and surface > potential calc/mapping > > > Dear List, > > > > Regards, > > Matthew Neiditch > > Postdoc > Hughson Lab > Princeton University > neidi...@molbio.princeton.edu > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
