In the PDB format, every atom should be a member of one of these 3 categories: protein, nucleic, hetero.
FirstGlance in Jmol has long highlighted any 'anomalous atoms' that do not belong to any of the above 3 categories. It appears to me that Jmol (for a long time, including the latest Aug 17 version) is not properly categorizing certain atoms. They show up as 'anomalous' in FirstGlance (marked with dots and a "?" by default). In each case, these are fragments of residues (some main chain atoms are missing). Is this a bug or a feature? Examples: 1flo DC17:H (phosphate only) 4gqj DG6:B 4s0n DT5:E 1h8s GLY112:B, ARG111:A, ALA243:B, ALA243:A (N only) 3eqc ALA220:A, CYS277:A, ASN382:A (N and CA only) In the last case, for example, this leads to the bizarre result select ASN and not protein 2 atoms selected If this is a feature, I can work around it by re-defining 'protein' as the 20 standard L amino acids plus the 20 D amino acids, and 'nucleic' as the standard nucleotides. That will still miss fragments of non-standard residues, but those will be less common. Thanks, Eric ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
