Eric, Jmol does not use atom serial numbers in state scripts. It uses atom indexes, but maybe that's what you were referring to. I could see how that would cause a problem if the file is being extracted from the PDB on the fly, and the underlying PDB file has changed atom order.
The only viable solution is to keep a local copy of the PDB file you are using and have the state script refer to that. (I'm surprised ProtoPedia doesn't do that.) Then it is no big deal if RCSB changes the PDB file -- your copy will still work with the script. I'm afraid there's no way to change Jmol to have a working script that works with PDB files that change structure. If the PDB files are changing, then all bets are off that the Jmol script will work on the changed PDB file. Another possibility would be to always load a PDB file into Jmol data model, then load it from there. This PDB data would be saved then with the Jmol script. But the script could be VERY large.... Bob On Sun, Mar 29, 2009 at 9:23 PM, Eric Martz <[email protected]>wrote: > > > >It may be worth suggesting a change in Jmol to avoid using atom > >serial numbers in state scripts, in case a future remediation again > >scrambles the serial numbers. > > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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
------------------------------------------------------------------------------
_______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
