Rolf Huehne wrote: >Bob Hanson wrote: > > >>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. >> * >> >> >> > >So it is handled by using this priority list (helix/sheet inferred from >example '1B7Y' where helix overrules sheet): > > helix > sheet > turn > > > Not quite. It doesn't matter at what point in the listing the turn is present, it is only processed after assigning helix or sheet, in the order in the file. Then the turns are processed, and only if the group has not been assigned is the group assigned a turn.
Q: Are you seeing any HELIX/SHEET overlap, or just sloppy assignment of the turns? >Q: What is the reasoning behind this priority list? > > > The principals are "First-to-be-read, first-assigned" for helix/sheet, and "Better something than nothing" for helix/turn or sheet/turn. >Q: Shouldn't such faulty information rather be discarded? > > > We have to deal with faulty information the best we can. I think that's the role of a viewer. We do that all in a variety of places in Jmol, and I think that is part of the secret of its success. I think if we discarded both characterizations there would be lots and lots of complaints about structures not showing as expected. Much of this was in response to Eric's thorough testing of Jmol 10 across a whole set of structures. There were some revisions done at that time, and as far as I know, all of Eric's questions were answered satisfactorily. As I recall, mostly what we were seeing was not so much overlap but the same ending group being listed in two categories. It seemed more reasonable (to me, and Eric, I think) to assign HELIX or SHEET to the full run listed, even if turn was listed as starting at one of the end positions. Bob >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
