Rolf Huehne wrote: >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" >> >> >> Sorry -- I was mistaken there. The CONECT block is certainly not ignored. Jmol reads that block and creates those bonds, then Jmol goes through the atoms again looking for more bonds. The problem I've been seeing, particularly with metal centers, is that Jmol adds bonds where none were indicated in certain HETATM situations. So, for example, in 5cev you get a bond between the two Mn atoms in the cluster. But I suggest Jmol shouldn't be adjusting those bonds at all.
What I did was to set it up so that Jmol's autobonding would not add any more bonds than indicated in a CONECT block to a HETATM mentioned in the CONECT block. That seems reasonable, I hope. It looks pretty good with 1blu -- much better Fe/S cluster than with previous Jmol versions. The bonus is that then we can restore just the CONECT bonds to see what are in the PDB file, using CONNECT PDB, and we can again add Jmol's bonds using CONNECT PDB AUTO, or we can totally ignore the CONECT records and start from scratch using CONNECT by itself. The slight problem I was having is that non-biologically minded people have used the PDB format for their own purposes, generally using CONECT to indicate all the bonds, and then still use ATOM records instead of HETATM. We don't want Jmol going over those bonds at all. There was a safeguard in there that I accidentally took out but have reinstated that added the condition: "Do not do autobonding if the number of bonds from PDB CONECT records is more than half the number of atoms." So I think that is taken care of. -- 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
