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 <[email protected]> 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 <[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]
>>> 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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