[phenixbb] Maximum Likelihood Method for Twinning

[Peter Zwart]

Hi Chris,

You are right of course; The infrastructural change needed to do this
in phenix will take considerable effort however.

regards
Peter


On 30 July 2014 10:05, Chris Fage <cdfage at gmail.com> wrote:
> On the topic of twin refinement, I think it would be useful to implement the
> input of multiple twin laws. Xtriage identified three twin laws, but I had
> to refine in Refmac5 because only one could be entered in Phenix.
>
> Thanks,
> Chris
>
>
> On Wed, Jul 30, 2014 at 12:33 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
>>
>> In terms of actual implementation I have this in mind:
>>
>> http://www.phenix-online.org/newsletter/CCN_2011_01.pdf
>>
>> "Maximum likelihood refinement of twinned structures", page 29.
>>
>> Of course that would not stop (me) from implementing better ideas should
>> they arrive. However the paper mentioned above pictures a clear image of the
>> problem that we are going to address.
>>
>> Pavel
>>
>>
>>
>> On 7/29/14, 12:30 PM, Chris Fage wrote:
>>
>> Thank you, Randy, Nat, and Peter. I'll keep an eye out for that pub.
>>
>> Best,
>> Chris
>>
>>
>> On Tue, Jul 29, 2014 at 7:59 AM, Randy Read <rjr27 at cam.ac.uk> wrote:
>>>
>>> Yes, we were hoping to make some generalisations and improvements before
>>> publishing this.  (Which we obviously haven’t gotten around to doing yet!)
>>>
>>> Randy
>>>
>>> -----
>>> 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
>>> Hills Road
>>> E-mail: rjr27 at cam.ac.uk
>>> Cambridge CB2 0XY, U.K.
>>> www-structmed.cimr.cam.ac.uk
>>>
>>> On 29 Jul 2014, at 13:44, Nathaniel Echols <nechols at lbl.gov> wrote:
>>>
>>> > On Mon, Jul 28, 2014 at 12:41 PM, Chris Fage <cdfage at gmail.com> wrote:
>>> > Can anyone please direct me to a literature reference describing the
>>> > maximum likelihood method for detection of twinning based on twin laws, as
>>> > implemented in phenix.xtriage?
>>> >
>>> > If you mean the twin fraction estimation, the code doesn't have
>>> > anything more helpful than this:
>>> >
>>> > Zwart, Read, Grosse-Kunstleve & Adams, to be published
>>> >
>>> > -Nat
>>> > _______________________________________________
>>> > phenixbb mailing list
>>> > phenixbb at phenix-online.org
>>> > http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>>
>>
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>
>
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-- 
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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PHENIX:   http://www.phenix-online.org
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