On Tue, October 25, 2005 7:49 am, Miguel said: > > Please comment on the following proposal: > * Jmol will support the 'HG11' version > * The Jmol pdbReader code will convert atom names that > match the following format: > <digit> H <alpha> <digit> -> H <alpha> <digit> <digit> > > Justification: > * No reason to promote the pdb format > * No reason to promote poor/incorrect nomenclature > * I think this is a practical solution > > I think that the alternative is to do nothing ... the parser is not going > to be fixed in the short term.
The PDB folks had to do something to fit within the archaic constraints of the pdb file format; that doesn't mean these hacks have to be promulgated. Far better is to: a) get the mmCIF files from the PDB when these are needed, b) if an existing pdb-format file is the only thing available then use the freely available (from Herb Bernstein's site) pdb2cif.pl converter to make an mmCIF version of it. This way the jmol parser can conentrate on doing a perfect job with the CIF syntax rather than having to hack around the pdb-format weirdnesses. Rich ------------------------------------------------------- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today * Register for a JBoss Training Course Free Certification Exam for All Training Attendees Through End of 2005 Visit http://www.jboss.com/services/certification for more information _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
