[phenixbb] Maximum Likelihood Method for Twinning

Chris Fage cdfage at gmail.com
Wed Jul 30 07:05:45 PDT 2014


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
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>>
>>
>
>
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