[phenixbb] Rigid body refinement at low resolution

Pavel Afonine pafonine at lbl.gov
Tue Dec 9 18:35:57 PST 2014

Hi Jianghai,

normally this shouldn't happen. I wonder what's going on.. Could you 
please send me inputs and I will have a look right away?


On 12/9/14 3:50 PM, Jianghai Zhu wrote:
> Hi all,
> I recently solved a complex structure at 8 Å. There are 3 molecules per asymmetric unit and each complex contains 8 domains. I was trying to do rigid body refinement in phenix.refine. However, all the rigid body refinement gave me worse Rfree, even at ultra-low resolution, and phenix.refine reversed the result to the original model. Anyway to make this rigid body refinement more stable? Is there a dampen factor in phenix.refine so that the program only moves a domain at a fraction of what it wants to, e.g. 1/2, 1/3… ?
> Thanks.
> Best,
> —Jianghai
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