.. _RESEQ: ``RESEQ`` --------- According to the PDB format, atoms in a protein are specified starting with the nitrogen of the -NH:sub:`2` end and ending with the atoms at the -COOH end. ``RESEQ`` will re-arrange the atoms into the standard PDB sequence. ``RESEQ`` is useful particularly after adding hydrogen atoms, see below. Because ``RESEQ`` changes the order of the atoms, further work is not possible, and the calculation is stopped after the new geometry is printed. 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 C\ :sub:`δ1` and C\ :sub:`δ2`.  This means that either one of these atoms might be chosen at random to be C\ :sub:`δ1`, 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. A `complete worked example of RESEQ `__ can be downloaded. This shows how ``RESEQ`` can re-arrange the sequence of atoms into the standard PDB sequence.  The example is used in validating MOPAC, and is much more complicated than most cases users are likely to encounter.  Compliance with PDB conventions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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`` `__.