[phenixbb] Phenix.refine bonds/angles rmsd

Pavel Afonine PAfonine at lbl.gov
Tue Apr 13 14:43:36 PDT 2010

Hi Rongjin,
> when I use phenix.refine to refinemy structure, the rmsd's ofbonds and
> angles are
> pretty large. My data is 2.3 A resolution.
> *******************
> REMARK Start: r_work = 0.2838 r_free = 0.2789 bonds = 0.029 angles = 2.002
> REMARK Final: r_work = 0.2407 r_free = 0.2466 bonds = 0.029 angles = 2.002
> ************************************************************************

really (just wondering)?
What I would be really worry is the difference between Rfree and Rwork,
which apparently is terribly small, indicating that there is something
wrong with either free-R flags or refinement strategy.

> I tried many options but none worked so far. Here are the optionsthat
> I tried:
> phenix.refine mtz_filepdb_file strategy=tls
> tls_group_selections.paramswxc_scale=0.3 wxu_scale=0.8
> phenix.refine mtz_filepdb_file strategy=tls
> tls_group_selections.paramsfix_wxc=0.3 fix_wxu=0.8
> phenix.refine mtz_filepdb_file strategy=tls
> tls_group_selections.paramsfix_wxc=0.3 fix_wxu=0.8 optimize_wxc=false
> optimize_wxu=false
> These gave the same refinement results. Any suggestions?

It's not surprising, because in all refinements above you did not refine
the coordinates at all. The keyword "strategy=tls" means you refined
B-factors only (more precisely, you did constrained anisotropic
refinement, called TLS refinement). And therefore using wxc_scale or
fix_wxc or optimize_wxc would not make any difference. Also,
optimize_wxc is set to False by default, so you don't need to explicitly
say it.

I would run it like this:

phenix.refine mtz_file pdb_file
strategy=tls+individual_adp+individual_sites tls_group_selections.params

and hope that this fixes the "problem".

Let me know if you have any questions!

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