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

Tom Terwilliger terwilliger at lanl.gov
Mon Dec 17 10:11:09 PST 2007

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...

-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

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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