[phenixbb] Anisotropic ADP

Pavel Afonine pafonine at lbl.gov
Sat Dec 16 16:21:18 PST 2006

Hi James,

Thanks for you question!
With the most recent phenix.refine (available through CCI APPS) you can 
refine atomic displacement parameters (ADP) as:

1) individual isotropic;
2) combination: TLS + individual isotropic ADP;
3) grouped (1 ADP per group);
4) any mix of "1)-3)"

for any selected part of you structure.

Technically you can refine individual anisotropic ADP as well; however 
we don't have restraints for them. This is in my to-do list and will be 
implemented in future.

> In my .def file I can set:
>  adp {
>     individual {
>       isotropic = None
>       anisotropic = chain a
>       force_all_to_be_refined_isotropically = True
>     }
> and get ANISO lines in my output pdb.  But I'm confused as to whether
> this is actually refining with individual anisotropic b's for chain a
> (analagous to refining with anisotropic temperature factors in
> refmac).  Should I be resetting the force_all... to false?

The lines above are correct. You also need to set  
Note that, depending on resolution of your data, unrestrained individual 
anisotropic ADP refinement can potentially result in unphysical ADPs for 
some atoms or increase in Rfree. If this is not the case for your model, 
you're fine then.

Let me know if you have any questions / problems!

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