THE

MANUAL

Chapter 1: Do not read this manual

• Introduction
• The Elves philosophy
• The Elves Credo

Chapter 1a: Supplemental

• Processer Elves

Chapter 2: Single-wedge frame data

• The Wedger Elves
• Autoindexing
• Indexing with denzo
• Collection Strategy
• Refining camera and crystal parameters
• Measuring intensities
• Wedger Elves How-To
• Scripts written by Wedger Elves

Chapter 3: Checking important spots

• The Spotter Elves
• I'll bet you didn't know...
• other kinds of movies
• Spotter Elves How-To

Chapter 4: Scaling data from multiple sources

• The Scaler Elves
• Advantages of Smooth Scaling
• The Reference Data Set
• Output Formats
• Free-R flags
• Solvent Content
• Metal Site-Finding Program Set-up
• Scaler Elves How-To
• Scripts written by Scaler Elves
• The Future of Scaler Elves

Chapter 5: Heavy atom refinement and phasing

• The Phaser Elves
• Finding the Heavy Atoms in the First Place
• Convergence Criteria
• The Reference Data Set
• Solvent Flattening
• Sign and Hand Ambiguities
• Finding More Sites
• Customizing
• Input File Formats
• Output Formats
• Phaser Elves How-To
• Scripts Written by Phaser Elves
• The Future of Phaser Elves

Chapter 6: Model-building and Refinement

• Running ARP/wARP
• Refmacer Elves How-To
• Scripts Written by Refmacer Elves
• The Future: Builder Elves

Chapter 7: Tips and tricks

• Neat-o unix commands
• Simple awk commands everyone should have
• Tricks for your shell scripts (explained)
• secure directory-tree transfer

Chapter 8: Crystallography basics

• Crystallography glossary
• The oscillation method of data collection
• Sources of error
• The heavy atom method of phasing
• What you know when

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