[phenixbb] Reducing R/R-free

[George Devaniranjan]

Hi Pavel,
Thank you.

If I wanted to compare a RCSB structure's highest resolution shell R with
my refined highest resolution shell R.

Do I generate a log file with the binned R *for the RCSB structure* by
running phenix.refine but with *strategy='none' *

or is there a way to generate these binned R factors for the deposited
structure without running a refine cycle with none as strategy?

Thank you,
George




On Tue, Jan 13, 2015 at 11:04 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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>
> 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
>> >>> http://phenix-online.org/mailman/listinfo/phenixbb
>> >>>
>> >>
>> >>
>> >> _______________________________________________
>> >> phenixbb mailing list
>> >> 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
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150113/7c0c9f83/attachment.htm>