Hi Kendall,
1. methionines are converted to MSE 2. I'd like to include a .cif file for b-mercapto-ethanol adducted cysteines: CME. The .cif file is one that works for phenix.refine (listed below). I suspect I am not writing the .eff file correctly:
refinement.pdb_interpretation.apply_cif_modification { data_mod = cme residue_selection = chain A and resid 530 residue_selection = chain B and resid 381 }
If the above set of parameters works with phenix.refine, then it should work in AutoBuild too. Just save refinement.pdb_interpretation.apply_cif_modification { data_mod = cme residue_selection = chain A and resid 530 residue_selection = chain B and resid 381 } in a file refinement_params.eff and run AutoBuild for example like this: phenix.autobuild data=w1.sca seq_file=seq.dat model=coords.pdb rebuild_in_place=True refine_eff_file=refinement_params.eff Why you think it doesn't work correctly from within phenix.autobuild ? Pavel.