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? Q: How is or should this be handled by Jmol? 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
