[phenixbb] Phenix.refine bonds/angles rmsd

Pavel Afonine PAfonine at lbl.gov
Wed Apr 14 09:03:04 PDT 2010

Hi Rongjin,

> I am refining another 3.3 A resolution structure. In coot I manually
> adjusted the model
> to have >95% residues inpreferred region in ramanchandran plot, but
> after refinement
> in Phenix only <80% residues in the preferred region and a lot more in
> the outlier region.
> This was wen I used the default refinement parameters "phenix.refine
> mtz_file pdb_file".
> R and R_free are 0.22/0.27 in this case.

you may want to consider:

- using secondary structure restraints;
- tightening restraints (using wxc_scale=...);
- using H atoms in refinement;
- doing some quick geometry regularization before refinement;
- fixing manually and excluding from refinement certain parts of your model.

You need to experiment and find empirically which combination of the
above options works in your case. I would appreciate if you share your
experience with this and tell us what worked for your in the end.


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