Hello,
 
 pymol finds the disulphide bonds very nicely when you load a pdb file.

 What I want is, to tell him not to do that. I need it for the fact that I need to set new values of  dihedrals  to the protein, and if there is a disulphide bond, then pymol just doesnt set the dihedrals. One way is to load the pdb file, then go to builder mode and then manually break the bond. and then execute the set dihedral command. But I wish to script it, so that I dont have to do it manually.

 Is there a way to do this, either putting builder commands in .pml scripts, or setting certain values, so that pymol doesnt look for sulphers.

 Thanks in advance,

Abhi