Hi Tom,
Thank you for the inf.
I have also read
https://www.phenix-online.org/presentations/ensemble_refinement_burnley_at_a...
result looks impressive.
It is running OK but slow (24h already), using submitted structure PDB ID 4CK4
George
From: Tom Burnley [mailto:[email protected]]
Sent: Monday, February 15, 2016 1:51 PM
To: George Kontopidis
Cc: PHENIX user mailing list
Subject: 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 mailto:[email protected]
Sent: Sunday, February 14, 2016 11:45
To: 'Billy Poon' mailto:[email protected] ; 'R. D. Oeffner' mailto:[email protected]
Cc: 'PHENIX user mailing list' mailto:[email protected]
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 tel:%28510%29%20486-5709
Fax: (510) 486-5909 tel:%28510%29%20486-5909
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 tel:%2B44%280%291223%20763234
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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