[phenixbb] ensemble refinement

[Tom Burnley]

Hi George,

Just in case you haven't seen it already - CCN from 2013 contains a case
study regarding optimal use of ER (p51).

https://www.phenix-online.org/newsletter/CCN_2013_07.pdf

Best wishes,

Tom

On 14 February 2016 at 20:25, George Kontopidis <gkontopidis at vet.uth.gr>
wrote:

> Done it.
>
> Now I can see ensemble refinement option.
>
> I would let you know how the results look like.
>
>
>
> Many thanks,
>
>
>
> George
>
>
>
>
>
> *From:* R. D. Oeffner [mailto:rdo20 at cam.ac.uk]
> *Sent:* Sunday, February 14, 2016 2:23 PM
> *To:* George Kontopidis
> *Cc:* 'PHENIX user mailing list'
> *Subject:* Re: [phenixbb] ensemble refinement
>
>
>
> You need to enable the “alpha test programs” options. Open the Phenix
> Preferences dialog, click the “General” button and scroll down to find it.
> Then close and restart Phenix.
>
>
>
> *From:* George Kontopidis <gkontopidis at vet.uth.gr>
>
> *Sent:* Sunday, February 14, 2016 11:45
>
> *To:* 'Billy Poon' <bkpoon at lbl.gov> ; 'R. D. Oeffner' <rdo20 at cam.ac.uk>
>
> *Cc:* 'PHENIX user mailing list' <phenixbb at phenix-online.org>
>
> *Subject:* RE: [phenixbb] ensemble refinement
>
>
>
> Hi Bill,
>
>
>
> Phenix version  dev-2313-000 (nightly builds) have been downloaded and
> installed.
>
> GUI (phenix.refine) refinement settings does not seem to have an ensemble
> refinement option.
>
>
>
> Regards,
>
>
>
> George
>
>
>
> *From:* Billy Poon [mailto:bkpoon at lbl.gov <bkpoon at lbl.gov>]
> *Sent:* Saturday, February 13, 2016 10:46 PM
> *To:* R. D. Oeffner
> *Cc:* George Kontopidis; PHENIX user mailing list
> *Subject:* Re: [phenixbb] ensemble refinement
>
>
>
> Hi George,
>
>
>
> You should use one of the newer nightly builds if you want to use the GUI
> since there have been updates to the GUI.
>
>
> --
>
> Billy K. Poon
>
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>
> Lawrence Berkeley National Laboratory
>
> 1 Cyclotron Road, M/S 33R0345
>
> Berkeley, CA 94720
>
> Tel: (510) 486-5709
>
> Fax: (510) 486-5909
>
> Web: https://phenix-online.org
>
>
>
> On Sat, Feb 13, 2016 at 10:51 AM, R. D. Oeffner <rdo20 at cam.ac.uk> wrote:
>
> It’s included as an alpha version in version 1.10.1-2155 so you’ll have to
> switch on that setting to make it available from the GUI. It also runs from
> the command line when you call phenix.ensemble_refinement.bat from the
> phenix command prompt.
>
> Do let us know about any issues as I don't think many people have used it
> in anger on Windows yet.
>
> Regards,
>
> Robert
>
> --
> Robert Oeffner, Ph.D.
> Research Associate, The Read Group
> Department of Haematology,
> Cambridge Institute for Medical Research
> University of Cambridge
> Cambridge Biomedical Campus
> Wellcome Trust/MRC Building
> Hills Road
> Cambridge CB2 0XY
>
> www.cimr.cam.ac.uk/investigators/read/index.html
> tel: +44(0)1223 763234
>
>
> From: George Kontopidis
> Sent: Saturday, February 13, 2016 18:29
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] ensemble refinement
>
>
>
>
> Does ensemble refinement run on Phenix version 1.10.1-2155 (for windows)
>
> If yes
>
> can it run from GUI or only using command line?
>
>
>
> George
>
>
>
>
>
>
>
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