Re: [ccp4bb] Follow up to twinning question

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

Previous message:
Subject: Follow up to twinning question
From: Brett Collins b {- dot -} collins {- at -} IMB {- dot -} UQ {- dot -} EDU {- dot -} AU
Date: 2009-06-22

Next message:
Subject: Re: Follow up to twinning question
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2009-06-22

Subject: Re: Follow up to twinning question
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-22

It is in general matter for debate what to do in these extreme cases.
When NCS rotation is parallel to the potential twin operator even if
twin is present electron density does not change much (at least not as
much as we would like). There are many cases where because of this
twinning was not noticed at all. However it did not change electron
density or conclusion you drawb from the derived model.

To compare twin and non-twin you need to do sufficient number of
cycles of refinement and model building. Then your R/Rfree may
indicate differences better.

When you do twin refinement you add only one parameter (in case of
hemihedral twinning: in general the number of extra parameters is
equal to the number of twin domains minus one). I am not sure
overfitting is a danger here.

Twin fraction 43% indicates that there might be strong twinning (when
twin fraction is refined to a value close to 50% then it could be
because of higher symmetry or twinning)

To refine properly in the cases like yours you need to select
reflections carefully accounting for rotational symmetry (twin or
otherwise). For example you can generate free reflections in higher
space group (e.g. P41212) and then expand to lower symmetry. This way
you make sure that twin (or ncs rotation) related reflections belong
to the same class (working or free). If you have not done this then
freeR may be misleading. refmac (and I am sure that other programs
also) try to make sure that twin related reflections belong to the
same class. But if you do not specify twin then two ncs rotation
related reflections may belong to two different classes and it may
obscure Rfree. In your case it seems that only in the P41212 case free
and working reflections are not related with symmetry.

Until you have done all these tests (making sure that free is generate
in higher space group, sufficient number of cycles of refinement and
perhaps model building) it would be difficult to say if you have
twinning. Looking at the statistics you give it seems that there is
not enough evidence to reject hypothesis that space group is P41212
( I do not consider freeR since they do not seem to be "free" enough)

I hope it helps

regards
Garib

On 23 Jun 2009, at 02:16, Brett Collins wrote:

> Dear all,
> I posted here recently regarding a potential twinning problem I had
> and got some very useful feedback.
>
> The summary of what happened is I had a crystal that appeared to be
> P42212 from systematic absences after scaling in SCALA (a,b,c;
> 118,118,192). Interestingly POINTLESS suggested P41212 (or P43212 as
> the best solutions), and PHASER could only find a solution in P41212
> (2 mol/asu). Cumulative intensity plots suggested twinning, as did
> phenix.xtriage, and refinement at 2.6 A resolution was stuck at R/
> Rfree of 25.5/32.0. (Rmerge 6.5%). Although people suggested using
> refmac with twin refinement, in P41212 no twin laws were identified
> in REFMAC or phenix.xtriage.
>
> I tried indexing in lower symmetry P222 (a,b,c; 118,118,192) (Rmerge
> 5.4 %). PHASER found a solution in p212121 (4 mol/asu). Refinement
> now proceeds to R/Rfree of 25.3/27.9.
>
> I tried additional twin refinement in in P212121 using REFMAC, which
> found the twin operator k,h,-l with fraction ~43%. However, R/Rfree
> only changed marginally (and suspiciously) to 25.6/26.9.
>
> Importantly, in each case the maps seem good and I can't discern any
> significant difference between them.
>
> My questions are
> (i) which (if any) solution should I trust?
> (ii) Is the drop in R factors in p212121 just because parameters/
> data ratio is less? i.e Am I just overfitting the data?
> (iii) Do I really have twinning?
>
> Cheers,
> Brett
>
>
> ################################
> Brett Collins, PhD
> Group leader
> Institute for Molecular Bioscience
> Level 3 North
> Queensland Bioscience Precinct
> The University of Queensland
> St. Lucia, 4072, Qld,
> AUSTRALIA
>
> e-mail: b.collins@imb.uq.edu.au
> phone: 61-7-3346-2043
> FAX: 61-7-3346-2101
> website: http://www.imb.uq.edu.au/index.html?page=82433
>
> Courier address:
>
> Institute for Molecular Bioscience
> Queensland Bioscience Precinct
> Building 80, Services Road
> University of Queensland
> St. Lucia, Brisbane
> Queensland, Australia 4072
> ################################
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Follow up to twinning question
From: Brett Collins b {- dot -} collins {- at -} IMB {- dot -} UQ {- dot -} EDU {- dot -} AU
Date: 2009-06-22

Next message:
Subject: Re: Follow up to twinning question
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2009-06-22