[phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild

[Tom Terwilliger]

Hi Dale,

You can set the inner resolution limit for density modification and 
model-building in autobuild with

dmax=20.

This is not handed to phenix.refine at present...I will add that.

-Tom T

At 11:46 AM 12/17/2007, you wrote:
>Dear Tom,
>
>     Does this handle the inner resolution limit as well as the outer?
>
>Dale
>
>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
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > 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 
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB