[phenixbb] Error when specifying anomalous scatterers in autosol.

[Tom Terwilliger]

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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>
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>
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