[phenixbb] Gap between R and Rfree

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Fri Feb 26 06:18:34 PST 2010


I second that, please add pdf, png or ps output as an option. In phenix
the GUI is a choice, not a prerequisite to using the suite. I would
welcome it if further development of the suite would adhere to this
philosophy. 

Cheers,

	Carsten

> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Simon Kolstoe
> Sent: Thursday, February 25, 2010 5:01 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Gap between R and Rfree
> 
> oh yes please Pavel (command line polygon/statistics overview) - could
> the output be a pdf or ps rather than just starting up the GUI?
> 
> Simon
> 
> 
> 
> On 25 Feb 2010, at 19:39, Pavel Afonine wrote:
> 
> > Hi Francis,
> >
> > in PHENIX GUI: "Validation" -> "PDB Statistics Overview"
> >
> > or:
> >
> > in PHENIX GUI: "Validation" -> "POLYGON"
> >
> > The underlying idea is published here:
> >
> > Crystallographic model quality at a glance. L. Urzhumtseva, P. V.
> > Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009)
> >
> > I can add a command line version if anyone is interested.
> >
> > Pavel.
> >
> >
> >
> > On 2/25/10 9:45 AM, Francis E Reyes wrote:
> >> Pavel
> >>
> >> What phenix utility produces such information?
> >> Thx
> >>
> >> FR
> >>
> >> On Feb 25, 2010, at 10:43 AM, Pavel Afonine <PAfonine at lbl.gov>
> wrote:
> >>
> >>> Hi Young-Jin,
> >>>
> >>> the distribution of R-factors for all structures in PDB refined at
> >>> resolutions between 2.4 and 2.6 A is following:
> >>>
> >>> Histogram of Rwork for all model in PDB at resolution 2.40-2.60:
> >>>   0.115 - 0.141      : 5
> >>>   0.141 - 0.168      : 69
> >>>   0.168 - 0.194      : 414
> >>>   0.194 - 0.220      : 955  <<<<< your structure
> >>>   0.220 - 0.246      : 695
> >>>   0.246 - 0.273      : 153
> >>>   0.273 - 0.299      : 25
> >>>   0.299 - 0.325      : 5
> >>>   0.325 - 0.352      : 0
> >>>   0.352 - 0.378      : 1
> >>> Histogram of Rfree for all model in PDB at resolution 2.40-2.60:
> >>>   0.146 - 0.178      : 3
> >>>   0.178 - 0.210      : 41
> >>>   0.210 - 0.242      : 404
> >>>   0.242 - 0.274      : 1104
> >>>   0.274 - 0.305      : 653   <<<<< your structure
> >>>   0.305 - 0.337      : 108
> >>>   0.337 - 0.369      : 8
> >>>   0.369 - 0.401      : 0
> >>>   0.401 - 0.433      : 0
> >>>   0.433 - 0.465      : 1
> >>> Histogram of Rfree-Rwork for all model in PDB at resolution
> >>> 2.40-2.60:
> >>>   0.002 - 0.012      : 28
> >>>   0.012 - 0.022      : 83
> >>>   0.022 - 0.031      : 232
> >>>   0.031 - 0.041      : 430
> >>>   0.041 - 0.051      : 458
> >>>   0.051 - 0.061      : 493
> >>>   0.061 - 0.071      : 298
> >>>   0.071 - 0.080      : 186
> >>>   0.080 - 0.090      : 85   <<<<< your structure
> >>>   0.090 - 0.100      : 29
> >>>
> >>> which I interpret as your Rwork is most likely good as well as
> >>> Rfree, but the gap Rfree-Rwork is too large meaning possible
> >>> overfitting.
> >>>
> >>> A few tips:
> >>> - if you have NCS - use it in refinement;
> >>> - optimize refinement target weights: a) automatically:
> >>> "optimize_wxc=true optimize_wxu=true", or b) manually using
> >>> wxc_scale and wxu_scale parameters;
> >>> - make sure you use the latest PHENIX version.
> >>>
> >>> Let me now if you have any questions.
> >>>
> >>> Pavel.
> >>>
> >>>
> >>> On 2/25/10 9:17 AM, Young-Jin Cho wrote:
> >>>> Hi everyone,
> >>>> I recently got a diffraction data and am trying to refine it. The
> >>>> question is whatever I did the gap between R and Rfree stay far
> >>>> away: .2140/.2982 around 2.5 A resolution. (water added and
> >>>> isotropic(individual_adp) and so on).
> >>>> Although I am redoing with many different approaches, if anyone
> >>>> can give me any comments or suggestions, it would be helpful.
> >>>>
> >>>> Thanks in advance,
> >>>>
> >>>> Young-Jin
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>>
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