[phenixbb] ADP restraints under TLS+individual ADP

Tristan Croll tristan.croll at qut.edu.au
Wed Sep 23 04:30:59 PDT 2015


When taking a structure I refined in Phenix (using a TLS + individual ADP model) into a different refinement package, a colleague noted a host of warnings related to mismatched B-factors between the sulfur atoms in disulfide bonds. If I understand correctly, this arises due to Phenix falling back to a Ulocal only ADP restraints scheme and, in particular, the choice to set

adp_restraints.iso.sphere_radius  = 2.0.

The length of a disulfide bond being 2.05A, this means that as long as the geometry is correct the B-factors of the two sulfurs are never restrained to each other under these conditions.



Tristan Croll
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
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