Dear Remie, PyMol considers both chain identifier (chainID, column 22 in a PDB file) as well as the Residue sequence number (resSeq, columns 23-26 in a PDB file) to show the order of arrangement. So, simply renaming chainID’s will not work. In addition to that you will also have to renumber the resSeq (i.e. all the atoms of the first residue in chain A should be numbered 1 and so on). There are several programs that can do this, pdbset in CCP4 suite, pdbeditor (http://www.bioinformatics.org/pdbeditor/wiki/) or even online (http://www.canoz.com/sdh/renumberpdbchain.pl).
Best regards, Avinash
