[phenixbb] Question about refinement group definition

[Shota Nakamura]

中村昇太

Pavel Afonine <pafonine at lbl.gov>: 

>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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