Hello, We've just started using phenix.refine and I'm a bit confused about whether anisotropic ADP's are actually being used or not. On the wiki (http://www.phenix-online.org/phenix_wiki/phenix.refine) it says: << phenix.refine is the macromolecular refinement engine of the Phenix suite. It features * Individual as well as grouped B factor refinement * Anisotropic or isotropic+anisotropic B factor refinement * TLS refinement
However, the documentation says (http://www.phenix-online.org/download/documentation/phenix/phenix/structure_...): << Current limitations * No restrained individual anisotropic ADP refinement
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? Can someone with more knowledge clarify this? Thanks, the program seems to be working great otherwise! James Alber Lab UC Berkeley
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 force_all_to_be_refined_isotropically=False 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! Cheers, Pavel.
participants (2)
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James Fraser -
Pavel Afonine