[phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild
terwilliger at lanl.gov
Mon Dec 17 10:11:09 PST 2007
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...
. 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.
>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
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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