On Dec 1, 2007 7:02 PM, Bob Hanson <[EMAIL PROTECTED]> wrote: > In reading the material Rolf sent, though, it seems clear to me that in > the case of PDB files, the CONECT information is principally for the HET > records. It's assumed that the viewer will properly bond all ATOM records. > > Q: Is that a correct reading?
http://www.wwpdb.org/documentation/format23/sect10.html: "CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues." This indeed indicates that 'principally' mostly used for HET records. > So if you do use "set autobond FALSE" you get something that really > isn't usable. In fixing the business with the multimodel CONECT, I had > to implement bond caching -- Jmol acquires the list of CONECT > information, then applies it to all models later. This is quite > different from what Jmol was doing before, and it just might allow for > another possibility. > > Q: Would it be better if autobond respected the CONECT records of the > originating file? Yes. The content of the file should have priority. Like always, it's tricky... The Jmol autobond is bond length based (or was), and as such easily applied to all atoms... not just "ATOM" atoms, but "HETATM" atoms too. The above reading suggests this should only be done for those atoms that are actually residue atoms... not sure about the exact definition of such atoms, and if that is a 1:1 match with "ATOM", but it certainly adds complexity. > That is, should autobond not start from scratch but, in the case of PDB > files, first apply those CONECT records, THEN do the rest of the bonding? > > Q: Is there EVER a time you want to completely ignore CONECT records and > start all over? Would then somehow NOT be correct in some way? no idea. > The penalty of implementing this is just the memory required to save the > CONECT information rather than tossing it out after the file is read. I am not sure if bond info can be applied 1:1 from one model to another... only works if the actual connectivity remains the same... more likely for NMR than other data, but does it apply generally? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
