[phenixbb] questions about using experimental phases in phenix.refine

Pavel Afonine pafonine at lbl.gov
Sat May 15 12:37:38 PDT 2021

Hi David,

> I'm trying to use experimental phases derived from an cryoEM density 
> map do
> carry out reciprocal space refinement in phenix.refine.
> I used phenix.map_box to get the map coefficients, and then the CCP4
> program chltofom (with the -colin-phifom flag) to create the HL 
> coefficients
> from F/PHI computed from the electron density map.
> 1. If I ask for the mlhl target, I get quite odd target values, e.g. 
> for a 2.9 Å data set:
> | normalized target function (mlhl) (work): 
> -5862.311069                     |
> | target function (mlhl) not normalized (work): -6438670043.811632
> and attempted refinements more or less destroy my protein and increases
> both the mlhl target value and the R-factors.  Is there an example 
> data set
> I could access to help me find out what I'm doing wrong?  (Using the ml
> target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, 
> seems to
> work well, and has a postive target function, but seems sub-optimal if 
> phase
> information is available.)

this is odd..

Normally you should use (example)

phenix.map_to_structure_factors map.mrc d_min=3.4

to convert map to structure factors. The MTZ file  from the command 
above should be ready for phenix.refine. It contains "Fobs", free-R 
flags and HL coefficients that represent map phase information.

MLHL target will be used in this case, it is implemented exactly as 
described in the original paper:

Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J. (1998). Acta 
Cryst. D54, 1285–1294.

> 2. Is there a way to do a "simple" least-squares refinement, minimizing
> sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are 
> treated as
> vectors?  Does the ls target perhaps do this if 
> use_experimental_phases=True?

No, this is not implemented.


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