[phenixbb] automatically changed refinement parameters

Sara Züger szueger at bioc.uzh.ch
Tue Feb 2 02:13:05 PST 2010

Hi Pavel,

thanks for your answer!

If there is an "easy" (and for you fast) way to clarify the parameters:


Then I would appreciate some explanation.



-----Ursprüngliche Nachricht-----
Von: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] Im Auftrag von Pavel Afonine
Gesendet: Montag, 1. Februar 2010 18:50
An: PHENIX user mailing list
Betreff: Re: [phenixbb] automatically changed refinement parameters

Hi Sara,

> When I run phenix v1.6 via the GUI, starting a fresh refinement session
> the main window (I do TLS+isotropic ADP refinement and 5 macrocycles,
> otherwise everything default), I saw these non-default refinement settings
> in the run, which I did not specify myself, but the program:

this is specific to "tls+individual_adp" strategy only. TLS+isotropic 
ADP refinement protocol is highly optimized by re-refinement of several 
hundreds structures from PDB to find the optimal refinement parameters. 
These parameters are coded in phenix.refine and currently cannot be 
changed. In future versions of PHENIX this will be changes to a user 
will be able to overwrite these automatically picked values. If you use 
"optimize_wxu=True" then the value for wxu_scale is adjusted to achieve 
the best Rfree and Rfree-Rwork.

Please let me know if you have any questions!

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