Rolf Huehne wrote: > Hi, > >I noticed that in the PDB file of PDB entry '1AMR' there are overlaps >between different secondary structure record types, e.g.: > > HELIX 13 HM PHE A 352 LYS A 355 1 > TURN 16 T16 ILE A 353 GLN A 356 TYPE I > >This was quite unexpected and I searched for such overlaps in all >remediated PDB format files of the PDB. My script detected overlaps in >2032 entries. A text file containing the PDB codes and the corresponding >number of overlapping residues is (temporarily) available at this URL: > >http://www.fli-leibniz.de/~rhuehne/jmol/analyze_sec_struct-2008_02_26b-overlap.txt > >(Note: The numbers are not always correct because for simplification and >speed-up I didn't took into account numbering irregularities in the >non-border residues of an element, like insertion codes or nice residue >number sequences like "28,328,29" in entry '1BLB'.) > >The full logfile is (temporarily) available at this URL: > >http://www.fli-leibniz.de/~rhuehne/jmol/analyze_sec_struct-2008_02_26b-log.txt > >Q: Are the Jmol developers aware of this problem? > > > yes
>Q: How is or should this be handled by Jmol? > > > * * We do turn first, because sometimes a group is defined * twice, and this way it gets marked as helix or sheet * if it is both one of those and turn. * >Regards, >Rolf > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry 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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
