ensemble refinement

George Kontopidis

13 Feb 2016 13 Feb '16

4:29 p.m.

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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R. D. Oeffner

13 Feb 13 Feb

4:51 p.m.

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

Billy Poon

6:46 p.m.

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

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

George Kontopidis

14 Feb 14 Feb

9:45 a.m.

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

R. D. Oeffner

10:22 a.m.

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

George Kontopidis

6:25 p.m.

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

Tom Burnley

15 Feb 15 Feb

9:50 a.m.

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

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

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

George Kontopidis

4:52 p.m.

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

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Billy Poon
George Kontopidis
R. D. Oeffner
Tom Burnley