[phenixbb] Error when specifying anomalous scatterers in autosol.

[Francis E Reyes]

Tom

Thanks for the quick reply. Now I get this error.


chem171-152-dhcp:RBD_rebuild_xtalclear_SG76 francisreyes$  
phenix.autobuild after_autosolPHENIX VERSION:  1.3  of  26-05-2008



                PHENIX autobuild  Fri Jun 27 13:44:38 2008


                The PHENIX developers include:

P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung,
T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo,
J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger, P.H.  
Zwart


                If you use PHENIX please cite:

Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.-W., Ioerger, T.R.,  
McCoy, A.J.,
Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K.,  
Terwilliger, T.C.
(2002).  PHENIX: building new software for automated crystallographic  
structure
determination.  Acta Cryst. D58, 1948-1954.



------------------------------------------------------------
Starting AutoBuild with the command:

phenix.autobuild after_autosol=True

Sending output to  AutoBuild_run_4_/AutoBuild_run_4_1.log


No matching array:  
scaling.input.xray_data.obs_labels=ScalAveragedSG_76_30_PHX

Possible choices:
   AutoBuild_run_4_/refinement_PHX.mtz:S,SIGS
   AutoBuild_run_4_/refinement_PHX.mtz:FP,SIGFP
   AutoBuild_run_4_/refinement_PHX.mtz:PHIB
   AutoBuild_run_4_/refinement_PHX.mtz:FOM

Please use scaling.input.xray_data.obs_labels
to specify an unambiguous substring of the target label.


********************************************************************************
Failed to carry out AutoBuild_set_up_build:

failure
********************************************************************************

On Jun 27, 2008, at 1:11 PM, Tom Terwilliger wrote:

> 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
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>
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>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

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