[phenixbb] Question about refinement group definition
Pavel Afonine
pafonine at lbl.gov
Tue Nov 20 20:39:04 PST 2012
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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