[phenixbb] strategy of refinement for a structure phased by bromide soaking
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Thu Jan 10 16:44:10 PST 2008
> 1-As Phenix started it generated a
> fobs_experimental_phases_free_Rflag.mtz file. I have been using this
> file and no longer my data.hkl file for further refinement.
> I would like to know why the best_solution after the automatic
> building run does not contain any of the Bromide ions. It has water
> molecules but no Bromide ions? What is the reason for that?
Since Tom Terwilliger is off-line through Jan 21 I dare to offer
a guess: transferring the heavy atoms to the refined model is
simply not implemented.
> 2-I have been refining against the mtz file I mentioned but without
> any of these Bromide ions and although the refinement is converging ,
> I suspect I have been doing something bad and wrong.
> Should I start my refinement again from the first best pdb after
> automatic building and include right away the bromide ions with
> simultaneous f_prime, f_double_prime and occupancy refinement for the
> anomalous scatterers?
I think I'd keep the current protein model, but I'd discard all waters
and add the Br before continuing with the refinement.
I think once the Br are in the PDB file they will survive when you
run the wizards.
More information about the phenixbb