A useful additional keyword is HTML; this generates a simple HTML web-page and a PDB file in a form that is useful for displaying protein structures using JSmol.
When ADD-H or SITE is used, changes are made to the number or locations of hydrogen atoms. In these two cases, RESEQ will be run automatically unless NORESEQ is present, so there is no need to add RESEQ. If the number or location of hydrogen atoms is changed outside MOPAC, RESEQ should be used. If a raw PDB file, i.e., a file from the Protein Data Bank, is used as a data set, then hydrogen atoms will be added automatically, and RESEQ will then be run automatically. To stop RESEQ being run, use a MOPAC data set, i.e., a data set with keywords, and add NORESEQ.
RESEQ sometimes re-arranges the atoms in unexpected ways. Consider phenylalanine, for example. In it, the sequence of atoms is uniquely defined except for Cδ1 and Cδ2. This means that either one of these atoms might be chosen at random to be Cδ1, and the choice might be different from that used in the starting data set. This should not cause a problem when resequenced proteins are compared using the GEO_REF option, because, during the calculation of RMS difference, ambiguities of this type are automatically resolved.
Also, if the protein has gaps where residues are missing, RESEQ might put the fragments into the wrong order, particularly if the residues in the protein have been re-arranged as the result of earlier operations. If the order of fragments is incorrect, use CVB to make dummy bonds that bridge the gaps and re-run. Suitable atoms are the N terminus of one residue and the C of carboxyl of the other residue.
The following operations are performed when RESEQ is used:
Within each residue, the order of atoms is: First, the four backbone atoms, N-Ca-C-O, then the side-chain non-hydrogen atoms, then the terminal oxygen atom, OXT, (if present), then the hydrogen atoms, in the order in which they occur. One exception is that the HXT atom, if present, might not be the last hydrogen atom.
Heterogroups are positioned after all protein and isolated amino acid moieties.
See also: RESIDUES, XENO, CHAINS, and START_RES.