[phenixbb] Reducing R/R-free
Pavel Afonine
pafonine at lbl.gov
Tue Jan 13 08:04:35 PST 2015
Hi George,
look in phenix.refine log file: it prints statistics in resolution bins
(R-factors, completeness, number of reflections, <F>, etc); so you can
take the number from highest resolution shell. Of course the definition
of "highest resolution shell" is somewhat arbitrary, and also depends on
how you do binning.
Pavel
On 1/13/15 6:48 AM, George Devaniranjan wrote:
> Hi,
>
> I am sorry to ask another question, this is related to the above hence
> following up on this thread.
>
> I can calculate R/R-free using the validation tool but how does one
> calculate the
>
> R factors for the highest resolution shell ?
>
> Thank you,
> George
>
>
>
> On Tue, Jan 13, 2015 at 2:31 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de
> <mailto:tg at shelx.uni-ac.gwdg.de>> wrote:
>
> Hi Pavel,
>
> I was puzzled and misled by the choice of terms and implied an intent
> that apparently wasn't there.
>
> Best,
> Tim
>
> On 01/12/2015 10:01 PM, Pavel Afonine wrote:
> > Hi Tim,
> >
> > it is a shame that I can't remember that particular paper where
> I think
> > Randy Read or Axel Brunger have demonstrated that phase error
> and Rfree
> > are well correlated. So if you get best Rwork and Rfree chances
> are you
> > also get best map too.
> >
> > All the best,
> > Pavel
> >
> > On 1/12/15 3:54 AM, Tim Gruene wrote:
> >> Dear George,
> >>
> >> what are the reasons why are you trying to reduce the R/Rfree
> instead of
> >> producing the best possible map?
> >>
> >> Best,
> >> Tim
> >>
> >> On 01/11/2015 11:24 PM, George D wrote:
> >>> Hi Phenix users,
> >>>
> >>> I was looking at the phenix-refine manual and it mentions running
> >>>
> >>> optimize_mask=true
> >>>
> >>> optimize_xyz_weight=true
> >>>
> >>> optimize_adp_weight=true
> >>>
> >>>
> >>> I was wondering what else I could try to bring the Rw/Rf down
> by 1-2%
> >>> if possible, just wondering if there are any other strategies
> I could
> >>> try.
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> George
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> >>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>>
> >>
> >>
> >> _______________________________________________
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> >
> >
>
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
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