[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
>> >>>
>> >>>
>> >>>
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>> >>>
>> >>
>> >>
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>> >
>>
>> --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>>
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>
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