# This example mutates every residue of a chain to alanine. # load a structure cmd.load("$TUT/1hpv.pdb") # activate the mutagensis wizard cmd.wizard("mutagenesis") # set target residue type cmd.get_wizard().set_mode("ALA") from pymol import stored stored.list = [] # generate our list of residues (CA-atoms) to mutate cmd.iterate("1hpv//A//CA", "stored.list.append(string.join([model,segi,chain,resi,name],'/'))") # now iterate through each residue for sele in stored.list: # pick a residue cmd.edit(sele) # notify the wizard about the picked residue cmd.get_wizard().do_pick(0) # apply the mutation cmd.get_wizard().apply() # update the screen, showing the mutation cmd.indicate("byres "+sele) cmd.refresh() # now close the wizard cmd.set_wizard() cmd.deselect()