[phenixbb] ADP restraints under TLS+individual ADP

Pavel Afonine pafonine at lbl.gov
Wed Sep 23 05:47:57 PDT 2015

Hi Tristan,

oh I can see how this may be a problem! I can change 
adp_restraints.iso.sphere_radius 2->2.5 since this is ad hoc anyway just 
to trick the sphere ADP restraints behave like simple similarity 
restraints in case of refining Ulocal.

It would be interesting to see the actual example, so if you could send 
me the files (off-list) that would be great!

Thanks for reporting this!

All the best,

On 9/23/15 04:30, Tristan Croll wrote:
> Hi,
> 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.
> Cheers,
> Tristan
> Tristan Croll
> Lecturer
> Faculty of Health
> School of Biomedical Sciences
> Institute of Health and Biomedical Engineering
> Queensland University of Technology
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