Re: [phenixbb] ensemble refinement

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 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:[email protected]] *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

*Sent:* Sunday, February 14, 2016 11:45

*To:* 'Billy Poon' ; 'R. D. Oeffner'

*Cc:* 'PHENIX user mailing list'

*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:[email protected] ] *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 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: [email protected] 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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