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
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