On Tue, Nov 20, 2012 at 12:41 PM, Subhani Bandara
I am refining a protein with metal-ligand complexes. Is it possible to refine only y coordinates for an atom (on two fold) while keeping X and Z fixed using Phenix? Also is there a way to calculate something like anomalous difference-difference map (Anomalous Fobs - Anomalous Fcalc) to identify any additional atoms bound at metal sites.
Not sure about the first question, but the answer to the second is yes, if you download the latest nightly build, phenix.refine is now able to output an anomalous log-likelihood gradient (LLG) map from Phaser, which will indicate where any unmodelled anomalous scattering is present. This is most useful if you use the group_anomalous strategy with any heavy atom selected (I would put S in this list), and I suspect you need to refine them separately for optimal results (i.e. each metal is its own group, rather than one group with the selection "element FE" or whatever it is). You can also get an LLG map from phenix.maps, but this simply guesses the anomalous scattering based on the wavelength, and will probably be noisier than if you refine f' and f''. -Nat