[phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild
terwilliger at lanl.gov
Mon Dec 17 10:51:20 PST 2007
You can set the inner resolution limit for density modification and
model-building in autobuild with
This is not handed to phenix.refine at present...I will add that.
At 11:46 AM 12/17/2007, you wrote:
> Does this handle the inner resolution limit as well as the outer?
>Tom Terwilliger wrote:
> > Hi Dale,
> > Thanks for the notes! Here is what is supposed to happen:
> > the autobuild wizard keeps all the data you supply.
> > resolution=2.2 will set the resolution of model-building and density
> > modification and refinement
> > refinement_resolution=2.3 will set the resolution for refinement to
> > 2.3 instead of the 2.2 defined by resolution=2.2
> > There is as you guessed a bug however somewhere in the communication
> > between the autobuild wizard and phenix.refine, so the
> > refinement_resolution did not get passed properly. I will fix that...
> > Thanks!
> > -Tom T
> > . At 01:29 AM 12/17/2007, Dale Tronrud wrote:
> >> The structure factors that I downloaded from the PDB for my
> >> little MR project contains both reflections behind the beam stop
> >> and reflections of higher resolution than even the original authors
> >> would use. When setting up the MR I entered the more restrictive
> >> resolution limits into the Wizard and Phaser appears to have obeyed.
> >> As near as I can tell from the log files, however, Resolve is
> >> using all the data in the rebuild. I am including a copy of the
> >> log file from the "best" refinement. I would prefer that only
> >> data between 30 and 2.2A were used but it is clear that the
> >> refinement is, at least, monitoring the fit to all the data. I
> >> am presuming that the program is refining against the same data
> >> it is monitoring.
> >> I would like to suggest that either the log file be clearer
> >> about the resolution limits it is actually refining to, or the
> >> plumbing that passes the resolution limits from the AutoMR wizard
> >> to the AutoBuild wizard be checked.
> >> Dale Tronrud
> >> P.S. That's all my problems... For now. The project I'm working
> >> on is cursed and brings out the worst in all the software I have
> >> used.
> > 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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> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
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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
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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