Phaser-2.3: Manual - Revision history

Airlie at 22:18, 1 August 2012

2012-08-01T22:18:58Z

WikiSysop: /* XML */

2012-06-27T15:14:03Z

‎XML

WikiSysop: /* Python */

2012-06-27T15:11:57Z

‎Python

WikiSysop: /* Keywords */

2012-06-27T15:10:58Z

‎Keywords

WikiSysop: /* Keywords */

2012-06-27T15:10:47Z

‎Keywords

Airlie: /* Keywords */

2012-04-24T13:04:23Z

‎Keywords

Airlie: /* Keywords */

2012-04-24T13:03:59Z

‎Keywords

Airlie: /* Keywords */

2012-04-24T12:59:10Z

‎Keywords

Airlie at 12:58, 24 April 2012

2012-04-24T12:58:30Z

Airlie: moved Phaser-2.3: Manual to Phaser: Manual: For version 2.3 and above

2011-10-19T09:31:11Z

moved Phaser-2.3: Manual to Phaser: Manual: For version 2.3 and above

New page

#REDIRECT [[Phaser: Manual]]

← Older revision		Revision as of 22:18, 1 August 2012
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	Please contact us for more information or XML output requests.		Please contact us for more information or XML output requests.
	;{{Oldid\|506\|XML}}		;{{Oldid\|506\|XML}}
		+
		+	==CCP4i==
		+	Download
		+	#Molecular Replacement [http://www-structmed.cimr.cam.ac.uk/phaser/Phaser_MR_3.tar.gz Phaser_MR_3.tar.gz]
		+	#Experimental Phasing [http://www-structmed.cimr.cam.ac.uk/phaser/Phaser_EP_3.tar.gz Phaser_EP_3.tar.gz]
		+	#Normal Mode Analysis [http://www-structmed.cimr.cam.ac.uk/phaser/Phaser_NMA_3.tar.gz Phaser_NMA_3.tar.gz]
		+	To install new Phaser GUI
		+	# Make sure you have '''write permission''' for the directory where ccp4 is installed
		+	# Start the CCP4 GUI (by entering "ccp4i" at the command line)
		+	# Select the "System Administration" pull-down on the right-hand side of the CCP4 gui
		+	# Select "Install Tasks"
		+	# In the new window, in the "Task archive" box, enter <path-to>/Phaser_MR_3.tar.gz. Note that the file '''must''' be called Phaser_MR_3.tar.gz − '''Do not rename it'''
		+	# The details of the Phaser gui installation will appear in the boxes
		+	# Click "Apply" at the bottom of the window
		+	# Click "Accept" in the prompt box
		+	To uninstall previous Phaser GUI
		+	# Make sure you have '''write permission''' for the directory where ccp4 is installed
		+	# Start the CCP4 GUI (by entering "ccp4i" at the command line)
		+	# Select the "System Administration" pull-down on the right-hand side of the CCP4 gui
		+	# Select "Install Tasks"
		+	# In the top pulldown, Select '''Run the Installation Manager to''' "uninstall an existing task"
		+	# In the new Choose Task to Uninstall folder, choose "Phaser". ''If there is no task called Phaser, you have not installed the ccp4i GUI for Phaser manually.''
		+	# The details of the Phaser gui installation will appear in the boxes
		+	# Click "Apply" at the bottom of the window
		+	# Click "Proceed" in the prompt box
		+	# Exit ccp4i
		+	New GUI will not rerun jobs with old GUI
		+	:Keyword input has changed. You cannot (reliably) rerun old phaser jobs in the new GUI (not backwardly compatible).

@@ Line 24: / Line 24: @@
 There is XML output available for developers writing automation scripts.<br>
 Please contact us for more information or XML output requests.
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=XML&oldid=506 XML]
+;{{Oldid|506|XML}}

@@ Line 14: / Line 14: @@
 ==Python==
 Phaser can be scripted using python.
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Run-Jobs&oldid=713 Python Run-Jobs]
+;{{Oldid|713|Python Run-Jobs}}
 : How to run Phaser from python and the functions relevant for each Run-Job
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Functions&oldid=979 Python Functions]
+;{{Oldid|979|Python Functions}}
 : Detailed descriptions of the functions
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&oldid=601 Python Example Scripts]
+;{{Oldid|601|Python Example Scripts}}
 : Copy and edit to start using Phaser from python

@@ Line 9: / Line 9: @@
 ; {{Oldid|937|Keywords}}
 : Detailed descriptions of the keywords
-; {{Oldid|737|Keyword Example Scripts]
+; {{Oldid|737|Keyword Example Scripts}}
 : Copy and edit to start using Phaser from keyword input

@@ Line 5: / Line 5: @@
 ==Keywords==
 Phaser can be run using CCP4-style keyword input
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Keyword_Modes&oldid=805 Keyword Modes]
+; {{Oldid|805|Keyword Modes}}
 : The different functions that Phaser can perform and the keywords relevant for each mode
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&oldid=937 Keywords]
+; {{Oldid|937|Keywords}}
 : Detailed descriptions of the keywords
-;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Keyword_Example_Scripts&oldid=737 Keyword Example Scripts]
+; {{Oldid|737|Keyword Example Scripts]
 : Copy and edit to start using Phaser from keyword input

← Older revision		Revision as of 12:58, 24 April 2012
Line 1:		Line 1:
−	#~~REDIRECT~~ [[Phaser: ~~Manual~~]]	+	<div style="margin-left: 25px; float: right;">__TOC__</div>
		+
		+	This is the documentation for Phaser–2.3. There are some changes between this version and previous versions so input scripts may need editing.
		+
		+	==Keywords==
		+	Phaser can be run using CCP4-style keyword input
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Keyword_Modes&oldid=805 Keyword Modes]
		+	: The different functions that Phaser can perform and the keywords relevant for each mode
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&oldid=977 Keywords]
		+	: Detailed descriptions of the keywords
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Keyword_Example_Scripts&oldid=737 Keyword Example Scripts]
		+	: Copy and edit to start using Phaser from keyword input
		+
		+	==Python==
		+	Phaser can be scripted using python.
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Run-Jobs&oldid=713 Python Run-Jobs]
		+	: How to run Phaser from python and the functions relevant for each Run-Job
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Functions&oldid=979 Python Functions]
		+	: Detailed descriptions of the functions
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&oldid=601 Python Example Scripts]
		+	: Copy and edit to start using Phaser from python
		+
		+	==XML==
		+	There is XML output available for developers writing automation scripts.<br>
		+	Please contact us for more information or XML output requests.
		+	;[http://www.phaser.cimr.cam.ac.uk/index.php?title=XML&oldid=506 XML]