This issue is a recent change. These fragmentary residues were properly categorized in Jmol 14.3.7_2014.09.20.
On 8/22/15 3:11 PM, Eric Martz wrote: > 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 > ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
