[phenixbb] low resolution data/parameter ratio

Pavel Afonine PAfonine at lbl.gov
Fri Aug 14 15:11:54 PDT 2009

Hi Gerwald,

> Two more quick questions:
> how would you identify the best strategy? 

I would look at Rfree and Rfree-Rwork, and maps of course. To help in 
deciding what are the "good / reasonable" values, use POLYGON (Acta 
Cryst. D65, 297-300 (2009)) (phenix.polygon), local real-space 
correlation (phenix.real_space_correlation). I think Nat bundled them 
all into his magic tool called phenix.validation with will do this and 
more (it is GUI based).

> I would aim for the lowest number of parameters with reasonably low 
> Rfree?

Yes, this sounds right in general.

> Does phenix report the total number of parameters refined anywhere in 
> the log?

It's trivial and not at the same time (at least the way I understand it, 
of course I might be very wrong). It's trivial to compute the number of 
refinable parameters given the strategy you choose, but how you will 
count the restraints which are kind of quasi-observables, and what about 
weight that if chosen too strong so it can turn the restraints into 


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