should be volume 62 rather than 26 B. DeLaBarre and *A.T. Brunger*, Considerations for the refinement of low resolution crystal structures, /Acta Crystallographica D/ *62*, 923-932 (2006). cheers- todd -----Original Message----- From: [email protected] on behalf of Pavel Afonine Sent: Mon 8/20/2007 8:40 PM To: PHENIX user mailing list Subject: Re: [phenixbb] low res structures and Phenix Here is a nice discussion about low resolution refinement: B. DeLaBarre and *A.T. Brunger*, Considerations for the refinement of low resolution crystal structures, /Acta Crystallographica D/ *26*, 923-932 (2006). Pavel. Tom Terwilliger wrote:
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] 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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