Care should be exercised in using RESEQ in that there is the possibility of atoms being re-arranged in unexpected ways. Consider phenylalanine, for example. In it, the sequence of atoms is uniquely defined except for Cd1 and Cd2. This means that either one of these atoms might be chosen at random to be Cd1, and the choice might be different from that used in the starting data set. The effect of this is that any attempt to calculate the RMS difference between two structures, one of which has been re-sequenced, is likely to give a nonsense result, even if hydrogen atoms are ignored in the RMS calculation.
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. To ensure that the order of fragments is correct, use CVB to make dummy bonds that bridge the gaps. Suitable atoms are the N terminus of one residue and the carboxyl of the other residue.
See also: xeno, residues, chains, and start_res.