As a follow-up -- Here is what I am experimenting with in Jmol 11.3.52: 1) loading of CIF files is no different 2) default loading of PDB files respects CONECT records, but adds to that set additional bonds to atoms that are not HETATM atoms or HETATM atoms but are not part of CONECT records. 3) the command "connect" by itself is same as always -- ignore CONECT and make all new connections 4) the command "connect PDB" shows the CONECT set of bonds 5) the command "connect PDB AUTO" does the same as the default PDB loading (2).
Thoughts? Bob Bob Hanson wrote: > Jmol users, > > Having properly implemented CONECT in PDB files, it occurs to me that > all along Jmol has not really properly handled these. This most recent > point was that a single CONECT block must apply to all models in an > NMR model set. And that is fixed. But there is an underlying issue here. > > When you load a PDB file into Jmol, certainly for most biomolecules > the CONECT block is completely ignored, and Jmol goes and creates its > own bonds instead. All CONECT information is ignored. This feature is > turned off using "set autobond FALSE" > > 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? > > 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? > > 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? > > 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. > > Advise, please. > > Bob > > > -- 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 ------------------------------------------------------------------------- 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
