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

David A Case david.case at rutgers.edu
Sat May 15 10:29:04 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 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.)

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?

Usual apologies if there is some great tutorial on this that I've not found.

...thanks...dave case

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