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Appion Manual » History » Version 20

Amber Herold, 04/22/2010 12:57 PM

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h1. Appion Manual
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# [[An Introduction to Appion]]
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## [[What is Appion?]]
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## [[System Requirements]]
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## [[Authors]]
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# [[Complete Installation]]
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## [[Instructions for installing CentOS on your computer]]
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## [[Download additional Software]]
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## [[Database Server Installation]]
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## [[Processing Server Installation]]
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### [[Install supporting packages]]
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### [[Download Appion Files]]
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### [[Perform system check]]
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### [[Install Appion Packages]]
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### [[Configure leginon.cfg]]
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### [[Explanation of Sample Names]]
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### [[Configure sinedon.cfg]]
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### [[Install External Packages]]
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### [[Compile FindEM]]
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### [[Compile Ace2]]
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### [[Compile Radermacher]]
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### [[Install Xmipp]]
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### [[Test Appion]]
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## [[Web Server Installation]]
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### [[Differences between Linux flavors]]
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### [[Install Web Server Prerequisites]]
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### [[Configure php.ini]]
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### [[Install Apache Web Server]]
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### [[Check php information]]
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### [[Install the MRC PHP Extension]]
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### [[Install the Web Interface]]
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### [[Potential Problems]]
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## [[Create a Test Project]]
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## [[Setup Remote Processing]]
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# [[Upgrade Instructions]]
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# [[Appion User Guide]]
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## [[Appion and Leginon Database Tools]]
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### [[Administration]]
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#### [[Groups]]
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#### [[Users]]
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#### [[Instruments]]
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#### [[Default Settings]]
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#### [[Calibrations]]
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#### [[Applications]]
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#### [[Goniometer]]
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### [[User Management]]
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#### [[Enable User Authentication]]
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#### [[New User Registration]]
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#### [[Retrieve Forgotten Password]]
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#### [[Modify Your Profile]]
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#### [[Logout]]
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### [[Project DB]]
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#### [[View Projects]]
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#### [[Create New Project]]
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#### [[Edit Project Description]]
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#### [[Edit Project Owners]]
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#### [[Create a Project Processing Database]]
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#### [[Unlink a Project Processing Database]]
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#### [[Upload Images to a new Project Session]]
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#### [[Share a Project Session with another User]]
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#### [[View a Summary of a Project Session]]
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#### [[Grid Management]]
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### [[Image Viewers]]
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#### [[Image Viewer]]
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#### [[2 Way Viewer]]
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#### [[3 Way Viewer]]
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#### [[Dual Viewer]]
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#### [[Image Tools]]
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### [[LOI - Leginon Observer Interface]]
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### [[RCT]]
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### [[Tomography]]
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### [[Hole Template Viewer]]
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## [[Appion Processing]]
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### [[Terminology]]
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### [[Common Workflow]]
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### [[Processing Cluster Login]]
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### [[Particle Selection]]
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#### [[Template Picking]]
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#### [[Dog Picking]]
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#### [[Manual Picking]] 
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### [[CTF Estimation]]
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#### [[Ace Estimation]]
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#### [[Ace 2 Estimation]]
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#### [[CtfTilt Estimation]]
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### [[Import Tools]]
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#### [[PDB tp Model]]
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#### [[EMDB to Model]]
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#### [[Upload Particles]]
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#### [[Upload Template]]
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#### [[Upload Model]]
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#### [[Upload More Images]]
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#### [[Upload Stack]]
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### [[Image Assessment]]
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#### [[Web Img Assessment]]
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#### [[Multi Img Assessment]]
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#### [[Run Image Rejector]]
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### [[Region Mask Creation]]
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#### [[Crud Finding]]
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#### [[Manual Masking]]