On Thu, Dec 19, 2013 at 12:06 PM, Joseph Noel
I guess what I really would like to do is to derive experimental phases from the two wavelengths and the arrangement of Yb and S atoms in the structure. I would like to just provide the known coordinates for each and then derive phases that I can then use as restraints in the refinement of the structure at the first wavelength (longer wavelength). I know how to do this the old way but how do I do it in Phenix.
Extract the Yb and S atoms into a separate PDB file (use PDBTools for this, keeping only "element Yb or element S", and use this as input for AutoSol along with your anomalous data. The output will include a file with Hendrickson-Lattman coefficients (calculated by SOLVE, if you have more than one wavelength). You'll probably want to turn off model-building, since that's where most of the runtime goes. Regarding difference map peaks around heavy atoms: anomalous refinement will definitely be helpful in this case, but I would probably save it for the very last round of refinement. You won't be able to use the MLHL target but you can refine parameters (coordinates, B-factor, f' and f'') for just the Yb atoms and leave the protein alone. (I doubt the rest of the model would change very much if you included it, though.) But I'm curious what the map really looks like, because heavy atoms can cause weird effects, especially if your data are not truly "complete". Supposedly the maximum-entropy treatment helps with this. PS. Ensemble refinement can now use MLHL too (in nightly builds). -Nat