Re: [phenixbb] Reducing R/R-free

13 Jan 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 mailto:[email protected]> 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
    >>> [email protected] mailto:[email protected]
    >>> http://phenix-online.org/mailman/listinfo/phenixbb
    >>>
    >>
    >>
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    >
--
    Dr Tim Gruene
    Institut fuer anorganische Chemie
    Tammannstr. 4
    D-37077 Goettingen
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