[phenixbb] phenix.automr ensemble/component question
Scott Classen
sclassen at lbl.gov
Fri Feb 13 14:13:41 PST 2009
Hi Phenixers,
I'm a bit confused about the proper syntax for my phenix.automr job.
This is probably a simple concept, but I'm running on 3 hours of sleep
as my kid was up all night, and my synapses aren't working so good.
I expect 2 copies of my protein per AU
My protein is composed of two domains
I have a single PDB search model for each domain
is either of these commands correct?
phenix.automr data=mydata.sca \
ensemble_1.coords=domain1.pdb \
ensemble_1.identity=95 \
ensemble_1.copies_to_find=2 \
component_1.mass=40579 \
component_1.component_copies=2 \
ensemble_2.coords=domain2.pdb \
ensemble_2.identity=95 \
ensemble_2.copies_to_find=2 \
component_2.mass=13410 \
component_2.component_copies=2
or
phenix.automr data=mydata.sca \
ensemble_1.coords=domain1.pdb \
ensemble_1.identity=95 \
ensemble_1.copies_to_find=1 \
component_1.mass=40579 \
component_1.component_copies=2 \
ensemble_2.coords=domain2.pdb \
ensemble_2.identity=95 \
ensemble_2.copies_to_find=1 \
component_2.mass=13410 \
component_2.component_copies=2
essentially I'm not really using an ensemble of search models, I only
have a single PDB for each domain. So should ensemble_1.copies_to_find
and ensemble_2.copies_to_find be set to 1 or 2?
Thanks,
Scott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Scott Classen, Ph.D.
SIBYLS Beamline 12.3.1
http://bl1231.als.lbl.gov
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Lawrence Berkeley National Laboratory
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Berkeley, CA 94720
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Beamline) 510.495.2134
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