>> * The Jmol pdbReader code will convert atom names that >> match the following format: >> <digit> H <alpha> <digit> -> H <alpha> <digit> <digit> >> > the example I posted shoes that 1HB -> HB2
Is it not the case that this violates the PDB recommendations? I thought that they were supposed to put the digit in the front only in the case where the atom name was more than 3 characters. > This may cause great confusion with the PDB users. The PDB causes great confusion for me. >> Justification: >> * No reason to promote the pdb format >> > it is human readable So is CIF, so is XML >> * No reason to promote poor/incorrect nomenclature >> * I think this is a practical solution >> > an alternative operator for IUPAC atom naming > RasMol> select *.1HB;A > Jmol> select *,HB2%A comma cannot be used because it is the 'or' operator in an expression context. >> I think that the alternative is to do nothing ... >> the parser is not going >> to be fixed in the short term. >> > a parser which ignores context of e.g. "." or ";" should be fixed in the > long run. The openrasmol use of ';' for model (chain?) will not be supported in Jmol. Jmol, like Chime, supports ';' as a statement terminator. Miguel ------------------------------------------------------- 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
