4.2 transform Russell, Barton transform transform seqlab transform perl "transform" 0 transfile Domain descriptions file produced by stamp/sorttrans/alignfit (-f) perl " -f $value" 1 stamp_trans_file perl 1 het Include hetero atoms. Hetero atoms are normally not included in the output. (-het) perl ($value)? " -het" : "" 2 hoh Include waters (-hoh) perl ($value)? " -hoh" : "" 2 graphics Graphics output (-g) perl ($value)? " -g" : "" 2 This mode puts all transformed coordinates into a single PDB file, and labels the chains for domains sequentially (after their order in the transformation file) with A, B, C.. etc. This allows fast analysis of the structures graphically (i.e. using Rasmol) since one need only colour each chain a different colour to see the superimposition. The default file for writing the coordinates using this mode is `all.pdb'. all_pdb perl $graphics all.pdb pdbfiles perl ! $graphics *.pdb