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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 29 Jul 2014, at 13:44, Nathaniel Echols wrote:

On Mon, Jul 28, 2014 at 12:41 PM, Chris Fage 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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 mailto:[email protected]> 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 tel:%2B44%201223%20336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 tel:%2B44%201223%20336827 Hills Road E-mail: [email protected] mailto:[email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk http://www-structmed.cimr.cam.ac.uk

On 29 Jul 2014, at 13:44, Nathaniel Echols mailto:[email protected]> wrote:

> On Mon, Jul 28, 2014 at 12:41 PM, Chris Fage mailto:[email protected]> 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 > [email protected] mailto:[email protected] > http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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 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 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

On 29 Jul 2014, at 13:44, Nathaniel Echols wrote:

...

On Mon, Jul 28, 2014 at 12:41 PM, Chris Fage 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb