[phenixbb] Phenix.refine on coordinate-optimised structures

Dorothee Liebschner dcliebschner at lbl.gov
Fri Aug 7 19:22:15 PDT 2020


The strategy depends also on the resolution of the data, so if you could
tell us that, we can give suggestions. Also the type of data, I guess X-ray

Out of curiosity, how do model quality metrics look like (clashscore,
ramachandran, etc) at this point? If you keep coordinates fixed, they won't
improve in refinement.

Best wishes,


On Fri, Aug 7, 2020 at 2:52 PM Joey Farrell <jpfarrell at uchicago.edu> wrote:

> Hello,
> I am trying to design a set of input parameters that I will be passing
> through the phenix.refine function. The structures
> that I am working with have already had their X,Y, and Z orthogonal Å
> coordinates optimised via separate protocol.
> I am looking for advice on which strategies and parameter values to use
> with phenix.refine to improve the crystallographic R-factors
> of such structures while preserving their earlier optimisation in real
> space.
> I have been having some success using “strategy =
> tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”,
> etc.) as
> well as adjusting the wxu_scale value until R-work and R-free are
> minimised. Are there other strategies or phenix.refine functionalities
> that may also prove helpful with this end in mind? I believe there may be
> ways to further improve R-work and R-free with this software
> that I am not yet aware of.
> Thank you for your help!
> Best,
> Joey
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