[phenixbb] Defining heavy atom sites for AutoSol

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jul 22 13:00:37 PDT 2010

Hi Kyle,
Yes, your guess is correct.   You could add "have_hand=True" if you know
the hand of the solution too.  You might also add 
"phaser_completion=False" if you really don't want any more sites added. 
On the other hand...usually phaser is pretty good at adding things that
are real, even if you might not recognize them as such at first, so you
might look carefully at the results that you get each way. We would be
interested in which turns out to be better!
All the best,
Tom T

>> Hi all,
>> I used AutoSol to generate SAD phases for a protein after completing a
>> partial MR model. My strategy worked, but I noticed there were more heavy
>> atom sites in the solution than I was expecting. Having continued to build
>> and refine the structure, I am fairly certain that I know which sites are
>> the real sites and which ones are noise. I would like to use the real
>> sites
>> to reproduce the experimental phases in AutoSol or another Phenix module
>> to
>> perhaps improve the map quality (essentially running just SOLVE or Phaser
>> without HYSS or model-building). What is the right approach? I am guessing
>> something like this:
>> phenix.autosol data.sca sequence.dat sites_file=sites.pdb build=False
>> Cheers,
>> Kyle
>> Kyle T. Dolan
>> Department of Biochemistry and Molecular Biology
>> The University of Chicago
>> ktd at uchicago.edu
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