[phenixbb] ramachanran plot refinement or restraint?

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Fri Jul 27 09:26:51 PDT 2007

Hi Jianghai,

> I tried "discard_psi_phi=False" in phenix.refine.  There is only  
> slightly improvement in the R, Rfree, and ramachandran plot (about  
> 0.2% less disallowed residues, wxc_scale=0.2).  A structure  
> optimization (wxc_scale=0) with the phi-psi restraints has a bigger  
> impact (about 2% less disallowed residues) with about 2% higher  
> Rfree.

Thanks for your feedback!

> What do you think is a good value for wxc_scale in a low-resolution
> refinement?

This is a tough one to answer. wxc_scale reflects how much you
trust your data to guide you to the best model. That depends on many
influences. I think the best - although expensive - approach is to
simply try a range of values.

Note that the esd on the psi-phi restraints are just someone's (?)
best guesses. It may be worth playing with these values as well.
For that, copy the data_link_TRANS, data_link_PTRANS, data_link_CIS,
and data_link_PCIS blocks from mon_lib_list.cif to a new files,
change the values, then specify the file on the phenix.refine
command line. (You may want to double-check in the .geo file
that your new values are actually used.)

> What is the difference between wxc_scale=0 and
> phenix.geometry_minimization?

Should basically be the same, but in phenix.refine you can override
parameters like discard_psi_phi. phenix.geometry_minimization doesn't
allow you to do this (it is one of those many little things I never
got to).


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