[phenixbb] questions about using experimental phases in phenix.refine
pafonine at lbl.gov
Sat May 15 12:37:38 PDT 2021
> 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
> 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
> 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
No, this is not implemented.
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