[phenixbb] Please help with neutron composite SA-omit

Anna Gardberg anna.s.gardberg at gmail.com
Mon Feb 23 12:12:26 PST 2009

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:

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:

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.


On Mon, Feb 23, 2009 at 2:46 PM, Thomas C. Terwilliger
<terwilliger at lanl.gov> 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
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>> phenixbb at phenix-online.org
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