[phenixbb] Error when specifying anomalous scatterers in autosol.

Tom Terwilliger terwilliger at lanl.gov
Fri Jun 27 14:01:00 PDT 2008


Hi again Francis,

Thanks for the several emails on the second half of this problem in  
which the input_refinement_file labels from a .sca file with a long  
name are not correctly interpreted.

This is caused by a known bug in version 1.3 rc2 of phenix. I'm sorry  
about that.

The general symptom is that the column labels are sometimes  
incorrectly assigned by autobuild if it cannot guess them correctly.

The best solution in your case (until we distribute the next version  
in which I have fixed this) is to rename your input_refinement_file   
to something very simple like "ref_data.sca" in which case the column  
labels will become ref_data and SIGref_data which will work fine.  If  
you have an input map coeffs file with non-obvious labels this can  
also happen...in that case you would have to rename the labels to  
really obvious ones like FP PHIM FOM.

  I tested this with dummy data and your file name of:

	input_refinement_file=ScalAveragedSG_76_30.sca

which failed

and replaced it with the same file, just renamed:

	input_refinement_file=ref_data.sca

which worked fine with this version.  Both work fine with the version  
that we have not yet distributed...


I hope that helps!
-Tom T


On Jun 27, 2008, at 1:45 PM, Francis E Reyes wrote:

> 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>> _______________________________________________
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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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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