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Appion Manual » History » Version 20

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

1 1 Amber Herold 
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]]