[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.


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list