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csymmatch pdbin-ref my_favorite.pdb pdbin the-other.pdb -origin-hand This should move the-other.pdb to overlay my-favorite.pdb It WONT relabel the Chain IDs though.. Eleanor On 12/13/2011 04:26 AM, intekhab alam wrote: > Hi All > > I have a 3.0A dataset of a protein-protein complex. I used one of the > protein structure solved previously as a template and used phaser in CCP4 > as well as in phenix. I used the sca file in phenix which gave a solution > with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used > the converted .mtz file which gave 6 molecules in ASU but with a different > packing. In both the cases map fits well in the model and there is some > extra density that may correspond to second protein partner of the complex > molecule. when i tried to use the MR solution generated in phenix with the > mtz file from ccp4 the model shows a lot of clashes. > > what kind of approach should i take so as to resolve this ambiguity. > > Regards