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
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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
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