Hi Francis,

Thanks!  I think the problem is here in your cif_def_file_list parameter file:

   anomalous_scatterers {
     group {
       selection = "name I"
       f_prime = -0.5783
       f_double_prime = 6.8299
     }
   }

where you are specifying the name I for anomalous scatterers...which seems perfectly reasonable, but....

unlike what you might expect, the anomalously-scattering atoms are not added to the PDB file created by AutoSol, so the I atom is not present during refinement and you get the error you show.

In AutoBuild, this should be added automatically, and if not, you can add it with

input_lig_file_list=my_ha_file.pdb

So yes, just go on to AutoBuild.  The build in AutoSol is really just to see if everything is working ok...not to do a real build. The default now is to use "helices_strands_only" so that this build goes very fast.

I hope that helps!

-Tom T

On Jun 27, 2008, at 12:20 PM, Francis E Reyes wrote:

------------------------------------------------------------
Starting AutoSol with the command:

phenix.autosol data=ScalAveragedSG_76_30.ref  
seq_file=seq_from_pdb.dat   \
refine_eff_file_list=./refinement/non_default.eff sites=2  
atom_type=I   \
f_prime=-0.582314 f_double_prime=6.84299 res_phase=3.4  
resolution_build=3.0   \
resolution=3.0 wavelength=1.5418 ha_sites_file=./ha_sites.pdb

Sending output to  AutoSol_run_7_/AutoSol_run_7_1.log


********************************************************************************
Failed to carry out AutoSol_build:

Refinement failed...perhaps something wrong with input refinement file
or data file or the column labels for them?
Error message from phenix.refine:
Empty atom selection:
  refinement.refine.anomalous_scatterers.group.selection="name I"
********************************************************************************


Cuts out in the first round of refinement (after initial Build_1.pdb) .

I guess I should not have specified anomalous scatterers (at least to  
autosol).

Does it refine anomalous automagically in the autobuild when doing a  
SAD via autosol?

How do I recover from this error?  (continue with the autobuild  
without anomalous scattering it now seems).


Thanks

FR
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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