[phenixbb] low res structures and Phenix
PAfonine at lbl.gov
Mon Aug 20 18:30:11 PDT 2007
> 1. Can Phenix do B-factor sharpening for improved maps?
This is not implemented in phenix.refine. CNS can do this.
> 2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix?
This is highly optimized in phenix.refine. I believe we have the most
sophisticated protocol for doing this (Acta Cryst. (2005). D61, 850-855,
"A robust bulk-solvent correction and anisotropic scaling procedure" P.
V. Afonine, R. W. Grosse-Kunstleve and P. D. Adams).
What you can try to do is to optimize the mask calculation parameters:
solvent_radius and shrink_truncation_radius (the default values are 1.11
and 0.9). To do specify in the command line (or in the parameter file,
whatever you use) one extra parameter: optimize_mask=True; for example:
% phenix.refine model.pdb data.mtz optimize_mask=True
This will tun much longer but may result in slightly improved statistics.
> 3. Are there any other suggestions for dealing with low resolution
> structures in Phenix?
How you refine the ADPs? TLS might be an option to try out.
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