[phenixbb] phenix.automr ensemble/component question

[Thomas C. Terwilliger]

Hi Scott,

Your first command looks good to me. It is saying that the composition of
the crystal is 2 copies of each chain:

component_1.component_copies=2 component_2.component_copies=2

and you want to search for 2 copies of each of your search models:

ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2

All the best,
Tom T


> 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.
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