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, Pavel 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 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443
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