[phenixbb] Reducing R/R-free

Pavel Afonine pafonine at lbl.gov
Wed Jan 14 15:52:24 PST 2015


Hi George,

phenix.refine outputs this statistics at the very beginning of 
refinement and at the end, so both pieces of information that you need 
are in one log file.

Pavel

On 1/13/15 8:24 AM, 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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