Hi... I'm performing a massive superposing of aminoacids in different conformations. The first model is a arginine "template" reference structure that is the fixed model in all matching iterations. I've loaded 236 models and i want to match the arginine guanidine group on the template guanidine. In each iteration i execute two matching, with different atoms selections. The first selection is the "right" selection: CD,NE,CZ,NH1,NH2 and the second is the "inverse" selection: CD,NE,CZ,NH2,NH1. I run the two superpositions, and i want to show that with the minimal RMSD between the guanidine groups. This is the code: import chimera from chimera import runCommand right = "@CD,NE,CZ,NH1,NH2" inverse = "@CD,NE,CZ,NH2,NH1" for i in range(2,328): print "Superposing..." runCommand("match #"+str(i)+right+" #0"+right+"; close 1") right_rmsd = runCommand("rmsd #"+str(i)+right+" #0"+right+"; close 1") runCommand("match #"+str(i)+right+" #0"+right+"; close 1") inverse = runCommand("rmsd #"+str(i)+inverse+" #0"+right+"; close 1") if right < inverse: print "Minimum RMSD =",right,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") elif right > inverse: print "Minimum RMSD =",inverse_rmsd,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") In principle this script should show the matching with the minimum RMSD, but it doesn't work. Please, help... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI