Re: [ccp4bb] Twin refinement - selecting FreeR Q for Garib..

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: "Martin {- dot -} Caffrey" martin {- dot -} caffrey {- at -} UL {- dot -} IE
Date: 2009-02-22

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Subject: Re: Could I improve an inconsecutive experimental map?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-02-23

Subject: Re: Twin refinement - selecting FreeR Q for Garib..
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-02-23

Is it true that when doing twinned refinement REFMAC does not use the
assigned FreeR set?

Eleanor

Roberto Steiner wrote:
> Hi Sabine,
>
> If your question is: Is it possible to refine twinned structures with
> Refmac?
> My answer is: Yes. Very well.
>
> Best wishes,
> Roberto
>
> On 20 Feb 2009, at 16:32, Sabine Schneider wrote:
>
>> Hi everyone,
>>
>> I got good data to 2.4A on a protein-ligand complex. I want to solve the
>> structure by MR using a model with 45% seq. ID and 55% similarity.
>> Initially the data appeared to be P622 (pointless, selfrotation function
>> etc). Unit cell: 145 145 65, MW protein is 28kDa
>> I prepared the MR model with chainsaw, choping of non-conserved residues
>> at the C gamma and reset the B-factors. Phaser found a solution, but
>> with negativ LLG.
>>
>> I than processed the data in P3, P321, P312 and P6 and run Phaser
>> searching all possible alternative spacegroups. The best solution is P3
>> (4mol/asu) followed by P321 (2mol/asu),both with a LLG of above 400. But
>> when trying to refine the models in Refmac the R/Rfree stays at ~48%.
>>
>> Looking at the truncate output and phenix xtriage, twinning is suggested
>> with the merohedral twin law -h, -k, l and a twin fraction of 40.3%
>> Using twin refine option in Refmac (5.5.0070), the R/Rfree for the P321
>> solution drops to around 33%, but the difference between R/Rfree is only
>> 1%. For the solution found in P3 the R/Rfree stays at around 47%.
>>
>> So I assumed that P321 is the better solution. Is the difference in
>> R/Rfree only 1%, because the free and work reflections are related
>> through the twin law?
>>
>> I used phenix to assign the free reflections putting in the twin
>> operators. Doing simulated annealing in phenix, I get a rather large
>> difference in R/Rfree of ~7%. Well, I guess I need to do some tweaking
>> of the parameters in phenix (running the latest phenix and cci_apps).
>> When I than use these free reflections assigned by phenix in Refmac I
>> still get only 1.5% difference between R and Rfree?
>>
>> So is it doable in Refmac, or is my best bet phenix? Any advice what is
>> the best way to proceed is much appreciated!
>>
>> Sabine
>>
>>
>> ------------------------------------------
>> Dr. Sabine Schneider
>> Ludwig-Maximilians-University
>> Department of Chemistry and Pharmacy
>> Butenandtstrasse 5-13, Building F
>> 81377 Munich
>> Germany
>> Phone: +49 (0)89 2180 77846
>> Fax: +49 (0)89 2180 77756
>> http://www.carellgroup.de/
>
> ---
> Roberto Steiner
> Randall Division of Cell and Molecular Biophysics
> New Hunt's House
> King's College London
> Guy's Campus
> London, SE1 1UL
> Phone +44 (0)20-7848-8216
> Fax +44 (0)20-7848-6435
> e-mail roberto.steiner@kcl.ac.uk
>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: Could I improve an inconsecutive experimental map?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-02-23