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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb