[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.
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