Re: [phenixbb] low resolution data/parameter ratio
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 quasi-constraints? Pavel.
One more detail I forgot to mention: to use most of the tools I mentioned you probably need to have recent PHENIX version (from nightly build at best): http://www.phenix-online.org/download/ Pavel.
On Aug 14, 2009, at 3:11 PM, Pavel Afonine wrote:
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).
These also get run in the phenix.refine GUI (phenix.validate simply repeats those analyses without refining). ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (2)
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Nathaniel Echols
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Pavel Afonine