[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
>     >>>
>     >>>
>     >>>
>     >>> _______________________________________________
>     >>> phenixbb mailing list
>     >>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     >>> http://phenix-online.org/mailman/listinfo/phenixbb
>     >>>
>     >>
>     >>
>     >> _______________________________________________
>     >> phenixbb mailing list
>     >> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     >> http://phenix-online.org/mailman/listinfo/phenixbb
>     >
>     >
>
>     --
>     Dr Tim Gruene
>     Institut fuer anorganische Chemie
>     Tammannstr. 4
>     D-37077 Goettingen
>
>     GPG Key ID = A46BEE1A
>
>
>     _______________________________________________
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>
>

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