<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<br>
<meta http-equiv="CONTENT-TYPE" content="text/html;
charset=ISO-8859-1">
Dear phenix developers, <br>
<br>
1) I would like to do paired refinement using the phenix refine gui.<br>
<br>
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.<br>
<br>
a, <br>
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)<br>
<br>
In the refinement setting strategy tab I uncheck everything and set
Number of cycles = 1.<br>
<br>
In “other options” I uncheck everything too.<br>
<br>
b,<br>
Alternatively adding a file to the input data with<br>
<br>
}<br>
<br>
xray_data {<br>
file_name = "/XYZ.mtz"<br>
labels = "FP,SIGFP"<br>
high_resolution = 1.8<br>
low_resolution = None<br>
outliers_rejection = True<br>
french_wilson_scale = True<br>
french_wilson {<br>
max_bins = 60<br>
min_bin_size = 40<br>
}<br>
<br>
refine {<br>
strategy = none<br>
sites {<br>
individual = None<br>
torsion_angles = None<br>
rigid_body = None<br>
}<br>
main {<br>
bulk_solvent_and_scale = True<br>
apply_overall_isotropic_scale_to_adp = True<br>
fix_rotamers = False<br>
flip_peptides = False<br>
nqh_flips = False<br>
use_molprobity = True<br>
simulated_annealing = False<br>
simulated_annealing_torsion = False<br>
ordered_solvent = False<br>
}<br>
<br>
should also do the same or have I overlooking something.<br>
<br>
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?<br>
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,.....”<br>
4. Additionally could one short comment on what phenix is doing with
strong (weak) reflections marked as aliens in XDS.<br>
<br>
5.<br>
According to the supplementary of P. Andrew Karplus, Kay Diederichs
“Linking Crystallographic Model and Data Quality” <br>
I would like to do <br>
anisotropic refinement, with additional options <br>
“ordered_solvent.new_solvent=anisotropic
<br>
adp.individual.anisotropic="not element H"
<br>
fix_rotamers=True”.<br>
<br>
Putting this in a file is enough?<br>
main {<br>
bulk_solvent_and_scale = True<br>
apply_overall_isotropic_scale_to_adp = True<br>
fix_rotamers = True<br>
flip_peptides = False<br>
nqh_flips = False<br>
use_molprobity = True<br>
simulated_annealing = False<br>
simulated_annealing_torsion = False<br>
ordered_solvent = True<br>
}<br>
refinement { <br>
refine { <br>
adp { <br>
individual { <br>
isotropic = none<br>
anisotropic = not element H<br>
} <br>
} <br>
} <br>
} <br>
<br>
<br>
The “problem” mentioned in phenix documentation is not a problem
with the gui?<br>
<br>
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). <br>
<br>
Thanks in advance and best regards, Georg.
<title></title>
<meta name="GENERATOR" content="LibreOffice 3.4 (Unix)">
<style type="text/css">
<!--
@page { margin: 0.79in }
P { margin-bottom: 0.08in }
TT.cjk { font-family: "WenQuanYi Micro Hei", monospace }
-->
</style><br>
</body>
</html>