[phenixbb] Fwd: MR-SAD, Yb, combined phases

Nathaniel Echols nechols at lbl.gov
Thu Dec 19 14:28:38 PST 2013

On Thu, Dec 19, 2013 at 12:06 PM, Joseph Noel <noel at salk.edu> wrote:

> 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).

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