[phenixbb] low res structures and Phenix
Tom Terwilliger
terwilliger at lanl.gov
Mon Aug 20 18:31:19 PDT 2007
Hi John,
I'll answer the first of your questions...
-Tom T
>I have a couple of questions regarding low res structures in Phenix
>(about 3.5 angstroms res).
>
>1. Can Phenix do B-factor sharpening for improved maps? If not
>what program do people usually use for this?
If you are using the AutoSol wizard, you can use the keywords:
correct_aniso=True b_overall=20.0
to force correction of any anisotropy in your data and to set the
overall B to 20.0. Note that this will affect all the maps produced
by the AutoSol wizard. I have not yet found this to improve the
quality of the resulting model; if it works for you please let me know!
You can also use phenix.xtriage to do this:
phenix.xtriage perfect.mtz hklout=output.mtz aniso.action=True
aniso.final_b=user_b_iso aniso.b_iso=77
will set the b_iso of perfect.mtz to 77
>2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix?
>
>3. Are there any other suggestions for dealing with low resolution
>structures in Phenix?
>
>Thanks,
>John Bruning
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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