Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

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

Previous message:
Subject: Shifting twin fraction with refinement - finally zero
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2010-04-23

Next message:
Subject: Re: Shifting twin fraction with refinement - finally zero
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-23

Subject: Re: Shifting twin fraction with refinement - finally zero
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-23

You may be using output reflection data from the previous cycle of
refinement for the next session. After twin refinement output Fobs
(confusingly) may be detwinned. You can try to use original reflection
data file (e.g. after scala/truncate/freerflag) and for refinement
and it may clarify things a bit. If you are using original reflection
data file for refinement then I do not knwo the reason of such
peculiar behaviour.

I have seen that twin fraction during refinement goes down but I am
not sure that it would happen substatioally if your R/Rfree were as
you stated before twin refinement.

regards
Garib

On 23 Apr 2010, at 22:28, hari jayaram wrote:

> I am refining a twinned dataset in possible spacegroup P212121 .
> Pointless thinks it is P43212 , but based on reading this posting (http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html
> ) I think it is P212121.
>
> The starting R/Rfree after molecular replacement ( single site
> mutant) was 34/38 to 2.2 A
>
> After an initial round of restrained refinement ( without twin
> refinement) and minimal rebuilding I got the R/Rfree to 30/34
>
> Then I did an amplitude based twin refinement - The twin fraction
> was 0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29
>
> After a little more rebuilding ( a few residues out of 800 residues
> in ASU) and another twin refinement I got an r/rfree of 22/27 . Now
> the twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)
>
> The maps looked a little better allowing me to fix a few more residues
>
> Finally the same twin refinement gives me no twin operators and the
> R/Rfree is 22/26
>
>
> All the twinning tests indicate a serious twinning in my crystal.
> Any ideas why I am seeing this
>
> Hari
>
>
>

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

Previous message:
Subject: Shifting twin fraction with refinement - finally zero
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2010-04-23

Next message:
Subject: Re: Shifting twin fraction with refinement - finally zero
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-23