[phenixbb] AutoSol question

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Jul 8 08:47:41 PDT 2011

Hi Laurie,

I'm sorry for the trouble!  If you provide a heavy_atom file then autosol
should not search for additional sites if everything is working ok.  In
the GUI you should be able to just supply the file and it should be
recognized.  On the command line you should be able to say


I just tried that here and it seemed fine. The log file said:

  HA SITES FILE /net/sigma/raid1/scratch1/terwill/misc/junk/wt056/ha.pdb
  Reading sites from 

If that doesn't work for you, can you send me (off-list;
terwilliger at lanl.gov) the full log file for your autosol run?  I'll have a
look at it.

Now a different question is finding sites closer together than you
specify.  You can say,

  hyss_min_distance = 3.5

to only look initially for sites 3.5 A apart with HYSS.  However phaser
will later try to add sites (if this is a SAD dataset) and they may be
closer than that (because they may simply be multiple conformations of a
SeMet side chain).

I hope that helps!
-Tom T

All the best,
Tom T

>> If I want to run Autosol with a set of previously determined heavy atom
>> positions (seleno-Met protein) that I might have edited, and NOT search
>> for
>> any more sites, just use those sites for phasing and density modification
>> and model building, I can't seem to find in any of the parameter buttons a
>> way to do this - every time I try it seems to just re-run hyss and find
>> the
>> same sites again.
>> It seems to find multiple Se sites on top of each other that are closer
>> than
>> the minimum distance I specified in the input.
>> Thanks
>> LAurie Betts
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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