[phenixbb] Please help with neutron composite SA-omit

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Feb 23 11:46:28 PST 2009

Hi Anna,

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


(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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