中村昇太 Pavel Afonine :

Hi Carsten,

some keywords have type "multiple" and some not. In your example, rigid_body has type multiple, that is you can specify as many of them as you want:

rigid_body = chain A rigid_body = chain B rigid_body = chain C

and that means you will be refining three rigid bodies. Same applied to tls, and many others.

anisotropic is not multiple, so it can be only one. I recall I had reasons to make it this way when implementing it but it was long long time ago, so I forgot what it was.

To see all attributes for all parameters: phenix.refine --show-defaults=all.all

which will yield a long hard to digest list.

Pavel

On 11/20/12 6:25 PM, Schubert, Carsten [JRDUS] wrote:

...

Hello all,

I have a question about the parameter definition for refinement groups (hope I picked the right term here). How does the definition and handling of refinement groups vary from the "refine.sites.rigid_body" scope to the "refine.adp.anisotropic" scope? For instance:

refine { strategy = *individual_sites individual_sites_real_space *rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = None torsion_angles = None rigid_body = chain A rigid_body = chain B } adp { individual { isotropic = None anisotropic = chain A anisotropic = chain B

}

would refine chains A and B as separate rigid groups, whereas only chain B would be refined anisotropically. Is this an intended behavior?

BTW "anisotropic = chain A or chain B" refines both chains as expected.

Cheers,

Carsten

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