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

Dale Tronrud det102 at uoxray.uoregon.edu
Mon Dec 17 10:46:13 PST 2007

Dear Tom,

    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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