Ben, Granted -- and there are certain times when it makes sense for everyone to be "wrong" in order to be consistent. But is this one such case? I think not. If DSSP "helices" aren't actually helices, then of what use is the standard? Neither the resulting statistics nor the cartoon figures will be correct.
I've put up one particularly egregious DSSP example on the web at http://www.pymol.org/not_helix for inspection. If you are comfortable with obvious turn regions (such as this one) being assigned as helix, then by all means, go right ahead and continue using DSSP via rTools or the PDB. But for me, I am not going to lose sleep over deviating from an existing standard in PyMOL. As I said before, the DSSP paper wasn't even written in such a way as to enable exact reproduction of their research other than by running their proprietary (1000 EURO) software program or by analyzing their source code. PyMOL's new "dss" algorithm is nowhere near validated enough to become a standard, but I do think that if we are going to agree upon a standard for secondary structure assignment, that the standard should reflect common notions of secondary structure, be exactly described, be reproducible, and be available in an open-source reference implementation. Does DSSP meet these criteria? No, but STRIDE might (if one could find it), and "dss" probably could in time. 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 Ben Hitz > Sent: Monday, November 03, 2003 8:28 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] DSSP > > > Warren - > The advantage of using DSSP over another heuristic method, is > that it is a standard. A DSSP helix is a DSSP helix > everywhere, even if a crystallographer might extend the end a bit. > > Ben > -- > Ben Hitz Exelixis > Computational Biology and Informatics > bh...@exelixis.com 650-837-8137 > > > > ------------------------------------------------------- > 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 >
