[phenixbb] refinement / alpha_beta
kay.diederichs at uni-konstanz.de
Tue Oct 5 11:30:30 PDT 2010
Dear Phenix developers,
I'd like to refine (using phenix.refine) a _very_ incomplete model
(obtained by molecular replacement with one subunit of the complete
structure) against the native amplitudes, with the goal to obtain
meaningful phases and figures_of_merit which should serve to find heavy
atom sites in derivative datasets.
If I "just refine" in phenix.refine, then the R-factors are in the 50s
and the program estimates the coordinate error to be very large. Thus I
would like to tell phenix.refine that the coordinates are actually quite
accurate, but that a lot of the model is simply missing.
method= *est calc
estimation_algorithm= *analytical iterative
in the documentation but I have trouble understanding its meanings and
defaults - but I do think this should be used. Maybe I should switch to
method=calc and specify number_of_macromolecule_atoms_absent= as well as
Can anyone advise me, please?
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