[phenixbb] Phenix.refine bonds/angles rmsd

guanrj at foxmail.com guanrj at foxmail.com
Wed Apr 14 10:00:19 PDT 2010

Thank you very much for your suggestions. I will try all these options and let you know
the results. 


= = = = = = = = On 2010-04-14 12:03:10 You wrote = = = = = = = = 
Hi Rongjin,

I am refining another 3.3 A resolution structure. In coot I manually adjusted the model
to have >95% residues in preferred 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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