Hi, Thomas. Thanks for the quick reply. When I try to implement your suggestion, a new AutoBuild directory is spawned. The AutoBuild_run_8_1.log file ends like this: WARNING: ERRORS IN RUN ...see AutoBuild_run_8_/WARNINGS_FROM_SUBPROCESSES Putting all omit results in AutoBuild_run_8_/OMIT OMIT results in AutoBuild_run_8_/OMIT : [] Combining all 16 omit regions in AutoBuild_run_8_/OMIT The file AutoBuild_run_8_/OMIT/overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 is missing...no composite omit made Possible operation: finished Required antecedents: [] Expected results: [] Application method: finished Yes, have antecedents... Resulting expectation:10000.0 Within the new directory, a TEMPO subdirectory (as well as others) containing several log files appeared. The log files all say something like this: ********************************************************************************Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_6_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... See AutoBuild_run_6_/LAST.LOG for more information ******************************************************************************** So, no luck yet. While awaiting further advice, I'm going to try it with my x-ray data, just to see if I can get that to work. Cheers, Anna On Mon, Feb 23, 2009 at 2:46 PM, Thomas C. Terwilliger wrote:

Hi Anna,

Try putting your cmmand "scattering_table=neutron" in a "refine.eff" file and then run phenix.autobuild including the keyword

refine_eff_file=refine.eff

(note that you may need to specify the scope of scattering_table just as if you were using the command directly for phenix.refine)

That is the way you can put any phenix.refine parameters into autobuild. Let me know if that doesn't do it! -Tom T

...

Hello.

I am attempting to create an SA-omit composite map with neutron scatterers.

Unfortunately,

phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" composite_omit_type=sa_omit scattering_table=neutron

results in an error:

"Sorry, unknown file or keyword: scattering_table=neutron Possibilities... (use 'phenix.autobuild --help all' to get full help): general.resolve_pattern_command_list=neutron density_modification.use_resolve_pattern=neutron decision_making.semi_acceptable_r=neutron decision_making.acceptable_r=neutron multiple_models.multiple_models_starting_resolution=neutron "

Can someone here help, please?

(For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. )

Regards, Anna Gardberg _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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