Configure cctbx.xfel from existing Phenix install - Revision history

Aaron at 22:02, 6 November 2018

2018-11-06T22:02:55Z

← Older revision		Revision as of 22:02, 6 November 2018
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			THIS PAGE IS DEPRECATED AND WILL BE DELETED

	Much of the code to run ''cctbx.xfel'' is already bundled in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured from an existing Phenix installation.		Much of the code to run ''cctbx.xfel'' is already bundled in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured from an existing Phenix installation.

Mona: I removed extra installation steps for prime.

2016-04-22T21:29:18Z

I removed extra installation steps for prime.

← Older revision		Revision as of 21:29, 22 April 2016
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	make		make

	~~prime.postrefine, one of the merging and scaling programs provided with ''~~cctbx.xfel~~'', requires~~ scipy. ~~This can be installed with this command:~~		All cctbx.xfel modules are now scipy free. The installation method described here should work without any installation of other third-party software.

	~~libtbx~~.~~python -m easy_install scipy~~

	~~On linux, this may require openssl to be installed, if it's not already:~~

	~~yum install openssl098e~~

Aaron at 18:19, 11 November 2015

2015-11-11T18:19:37Z

← Older revision		Revision as of 18:19, 11 November 2015
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	cd <path to phenix installation>/modules		cd <path to phenix installation>/modules
	git clone ~~git@~~github.com:dials/dials.git		git clone https://github.com/dials/dials.git
	cd ../build		cd ../build
	libtbx.configure xfel		libtbx.configure xfel

Aaron at 06:27, 27 October 2015

2015-10-27T06:27:07Z

← Older revision		Revision as of 06:27, 27 October 2015
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	cd <path to phenix installation>/modules		cd <path to phenix installation>/modules
	~~svn co https~~:~~//svn.code.sf.net/p/~~dials/~~code/trunk~~ dials		git clone git@github.com:dials/dials.git
	cd ../build		cd ../build
	libtbx.configure xfel		libtbx.configure xfel

Aaron at 00:11, 27 October 2015

2015-10-27T00:11:38Z

← Older revision		Revision as of 00:11, 27 October 2015
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	cd <path to phenix installation>/modules		cd <path to phenix installation>/modules
	svn co https://svn.code.sf.net/p/dials/code/trunk dials		svn co https://svn.code.sf.net/p/dials/code/trunk dials
	cd ..~~/modules~~/build		cd ../build
	libtbx.configure xfel		libtbx.configure xfel
	make		make

Aaron at 20:33, 11 August 2015

2015-08-11T20:33:58Z

← Older revision		Revision as of 20:33, 11 August 2015
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	make		make

	prime.postrefine, one of the merging and scaling programs provided with ''cctbx.xfel'' requires scipy. This can be installed with this command:		prime.postrefine, one of the merging and scaling programs provided with ''cctbx.xfel'', requires scipy. This can be installed with this command:

	libtbx.python -m easy_install scipy		libtbx.python -m easy_install scipy

Aaron at 20:33, 11 August 2015

2015-08-11T20:33:43Z

← Older revision		Revision as of 20:33, 11 August 2015
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	Note: this only applies to processing individual stills. Functionality to read XTC streams from LCLS is not included when using this procedure.		Note: this only applies to processing individual stills. Functionality to read XTC streams from LCLS is not included when using this procedure.

	Once Phenix is installed:		Once Phenix is installed and sourced correctly:

	cd <path to phenix installation>/modules		cd <path to phenix installation>/modules
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	make		make
	make		make

			prime.postrefine, one of the merging and scaling programs provided with ''cctbx.xfel'' requires scipy. This can be installed with this command:

			libtbx.python -m easy_install scipy

			On linux, this may require openssl to be installed, if it's not already:

			yum install openssl098e

Aaron: Created page with "Much of the code to run ''cctbx.xfel'' is already bundled in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured fro..."

2015-08-11T19:49:44Z

Created page with "Much of the code to run ''cctbx.xfel'' is already bundled in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured fro..."

New page

Much of the code to run ''cctbx.xfel'' is already bundled in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured from an existing Phenix installation.

Note: this only applies to processing individual stills. Functionality to read XTC streams from LCLS is not included when using this procedure.

Once Phenix is installed:

cd <path to phenix installation>/modules
svn co https://svn.code.sf.net/p/dials/code/trunk dials
cd ../modules/build
libtbx.configure xfel
make
make