Re: [phenixbb] Reducing R/R-free

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 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 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:

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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:

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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:

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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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