[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?
>John Bruning
>phenixbb mailing list
>phenixbb at phenix-online.org

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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