[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
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
C) 510.206.4418
O) 510.495.2697
Beamline) 510.495.2134
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~







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