[phenixbb] Reducing R/R-free

Georg Mlynek georg.mlynek at univie.ac.at
Tue Jan 13 18:30:36 PST 2015


Hi George, phenix.model_vs_data 
http://www.phenix-online.org/documentation/reference/model_vs_data.html 
is giving you statistics in resolution bins. The gui name is 
comprehensive validation.



On 01/13/2015 05:24 PM, George Devaniranjan wrote:
> 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 
> <mailto: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 <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
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>>         >> 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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