[phenixbb] SIR with sites from SAD?

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jul 17 09:03:24 PDT 2008

Hi Francis,

You can run autosol from the GUI and select "another dataset" as "YES" on
the first page.  Then you can put in the SAD and the SIR datasets, and
then on a later screen you can tell the wizard to read in the heavy-atom
sites for the SAD dataset i (or it can find them again). Then it will use
the sites from the sad dataset to find the sites for the sir dataset.

You can also do this from a script...the best example that is close to
your case is $PHENIX/phenix/phenix/wizard_scripts/AutoSol.mir . You can
then add to the lines where you are reading in the SAD data something

read_sites True
ha_sites_file   sites.xyz                  # the file with heavy-atom sites

However I am not sure that this is going to solve the problem because if
your map is uninterpretable from the SAD dataset ...then the difference
Fouriers for the SIR dataset may be uninterpretable too...


> I have a SAD dataset where autosol was able to find sites, but the
> resulting density modified map was uninterpretable. The unit cell for
> this SAD set was Unit cell: (53.2373, 53.2373, 186.446, 90, 90, 90)
> .
> I now have a heavy atom derivative. What's the format of autosol.inp
> (to be passed to phenix.runWizard AutoSol) that allows me to use the
> heavy atom sites from the SAD set as a basis for helping find heavy
> atom sites in the heavy atom derivative? Is it the same as SIR, except
> use ha_sites_file for the SAD solution?
> Native unit cell: [53.155600000000007, 53.1556000
> 00000007, 187.37970000000001, 90.0, 90.0, 90.0
> Derivative unit cell: [53.1
> 82299999999998, 53.182299999999998, 187.59569999999999, 90.0, 90.0,
> 90.0].
> Thanks
> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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