Bob Hanson wrote: > Rolf Huehne wrote: >>> >> 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? >
If I exlude TURN from the analysis there still remain 567 entries with HELIX/SHEET overlap. Many of those are overlapping only at one of the border residues but there are also cases with larger overlaps. These include helix fully inside sheet (e.g. 1B7Y) and sheet fully inside helix (e.g. 1DE8). By the way there are also examples with larger overlaps with turns (e.g. 1AMR). >> 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. > I analyzed now also the record order and it is the same for all entries: HELIX, SHEET, TURN So I don't think this can be used as a criterium. 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
