[phenixbb] paired refinement in phenix gui

Georg Mlynek georg.mlynek at univie.ac.at
Mon May 27 09:54:47 PDT 2013


Dear phenix developers,

1) I would like to do paired refinement using the phenix refine gui.

It would be nice if you could confirm if my settings are ok, or if there 
are still some settings in the background which I overlooked, because we 
see small changes in R and Rfree.

a,
I added the model refined at higher resolution (e.g. 1.5A) and the mtz 
file cut at CC (e.g.1.5A) in the "Input data" tab, and set High 
resolution cutoff in "X-ray data and experimental phases" box to (e.g. 1.8A)

In the refinement setting strategy tab I uncheck everything and set 
Number of cycles = 1.

In "other options" I uncheck everything too.

b,
Alternatively adding a file to the input data with

  }

     xray_data {
file_name = "/XYZ.mtz"
labels = "FP,SIGFP"
high_resolution = 1.8
low_resolution = None
outliers_rejection = True
french_wilson_scale = True
french_wilson {
max_bins = 60
min_bin_size = 40
   }

refine {
strategy = none
     sites {
individual = None
torsion_angles = None
rigid_body = None
     }
main {
bulk_solvent_and_scale = True
apply_overall_isotropic_scale_to_adp = True
fix_rotamers = False
flip_peptides = False
nqh_flips = False
use_molprobity = True
simulated_annealing = False
simulated_annealing_torsion = False
ordered_solvent = False
}

should also do the same or have I overlooking something.

2. For whatever reason I would like to do that (molprobity) - can I (and 
how can I do this)  add the command line commands also in the gui?
3. In december 2012 there was a discussion about weak data and 
refinement. I would like to know if there are new data available showing 
that "Whether the benefit they describe is considered cosmetic or 
non-trivial,....."
4. Additionally could one short comment on what phenix is doing with 
strong (weak) reflections marked as aliens in XDS.

5.
According to the supplementary of P. Andrew Karplus, Kay Diederichs 
"Linking Crystallographic Model and Data Quality"
I would like to do
anisotropic refinement, with additional options
"ordered_solvent.new_solvent=anisotropic
adp.individual.anisotropic="not element H"
fix_rotamers=True".

Putting this in a file is enough?
main {
bulk_solvent_and_scale = True
apply_overall_isotropic_scale_to_adp = True
fix_rotamers = True
flip_peptides = False
nqh_flips = False
use_molprobity = True
simulated_annealing = False
simulated_annealing_torsion = False
ordered_solvent = True
}
refinement {
   refine {
     adp {
       individual {
         isotropic = none
         anisotropic = not element H
       }
     }
   }
}


The "problem" mentioned in phenix documentation is not a problem with 
the gui?

it is a good idea to constantly monitor the existing solvent molecules 
and check for new ones by using ordered_solvent=true keyword. If it's 
decided to refine waters with anisotropic ADP then make sure that the 
newly added ones are also anisotropic; 
useordered_solvent.new_solvent=anisotropic (default is isotropic).

Thanks in advance and best regards, Georg.
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