Difference between revisions of "Phaser-2.3: Manual"

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(Python)
 
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There is XML output available for developers writing automation scripts.<br>
 
There is XML output available for developers writing automation scripts.<br>
 
Please contact us for more information or XML output requests.
 
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}}
 +
 
 +
==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).

Latest revision as of 22:18, 1 August 2012

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

Keyword Modes
The different functions that Phaser can perform and the keywords relevant for each mode
Keywords
Detailed descriptions of the keywords
Keyword Example Scripts
Copy and edit to start using Phaser from keyword input

Python

Phaser can be scripted using python.

Python Run-Jobs
How to run Phaser from python and the functions relevant for each Run-Job
Python Functions
Detailed descriptions of the functions
Python Example Scripts
Copy and edit to start using Phaser from python

XML

There is XML output available for developers writing automation scripts.
Please contact us for more information or XML output requests.

XML

CCP4i

Download

  1. Molecular Replacement Phaser_MR_3.tar.gz
  2. Experimental Phasing Phaser_EP_3.tar.gz
  3. Normal Mode Analysis Phaser_NMA_3.tar.gz

To install new Phaser GUI

  1. Make sure you have write permission for the directory where ccp4 is installed
  2. Start the CCP4 GUI (by entering "ccp4i" at the command line)
  3. Select the "System Administration" pull-down on the right-hand side of the CCP4 gui
  4. Select "Install Tasks"
  5. 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
  6. The details of the Phaser gui installation will appear in the boxes
  7. Click "Apply" at the bottom of the window
  8. Click "Accept" in the prompt box

To uninstall previous Phaser GUI

  1. Make sure you have write permission for the directory where ccp4 is installed
  2. Start the CCP4 GUI (by entering "ccp4i" at the command line)
  3. Select the "System Administration" pull-down on the right-hand side of the CCP4 gui
  4. Select "Install Tasks"
  5. In the top pulldown, Select Run the Installation Manager to "uninstall an existing task"
  6. 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.
  7. The details of the Phaser gui installation will appear in the boxes
  8. Click "Apply" at the bottom of the window
  9. Click "Proceed" in the prompt box
  10. 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).