Dear Jacob,
MR actually works pretty well with twinned data. There's some loss of signal, so that the model has to be a bit better to get a solution than you might have needed for untwinned data, but it doesn't seem to be a huge problem for anything but really marginal cases. So, although we've thought about implementing twin targets for MR in Phaser, it has always been a lower priority than other things that cause greater difficulties. (Not to mention the fact that really doing this properly, including accounting for what happens when a pseudosymmetric crystal is twinned — a not uncommon combination — is not trivial.)
A bigger problem, when you have perfectly twinned data, is determining the right space group, because you don't know what apparent symmetry comes from the twin operator. For that reason, Airlie McCoy recently implemented a new feature in Phaser so that it tells you all the subgroups of the current space group, any of which could be the true space group in the presence of twinning. Then you can run subsequent jobs in Phaser specifying one of these subgroups, and Phaser will expand the data to the lower symmetry before carrying out an MR calculation in that lower symmetry. As another way of dealing with this within a pipeline, where you can run numerous jobs simultaneously, Gabor Bunkoczi has made a tool that prepares all the MTZ files corresponding to subgroups.
All the best,
Randy
> On 3 Sep 2015, at 21:58, Keller, Jacob <[log in to unmask]> wrote:
>
> I have been trying to think of some reason why twinning could not be handled easily by MR algorithms, since we understand how twinning works and there's only one extra parameter (twin fraction alpha) to fit. Is it just something that's on the list but has not yet happened, or is there something more subtle to it that I am not thinking of? Yes, one can do MR on twinned data without accounting for twinning, but I would think the solutions would be much more obvious with twinning built in, and this would probably make a big difference in marginal cases.
>
> Even SAD might be workable when the twin operator doesn't superimpose all Bijvoet mates on each other (I think this is possible).
>
> All the best,
>
> Jacob Keller
>
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> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
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Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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