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ChimeraX User Guide: General Topics

• Documentation Index
• Tutorials
  included with download (others online)

  • Quick Start Guide
  • Protein-Ligand Binding Sites
• Startup
• ChimeraX Window and Menu
• Data Formats: see open and save
• Manipulation: see mousemode
• Selection
• Measurements
• Making Images
• Making Movies
• Virtual Reality
• Settings (Preferences)
• Citing ChimeraX

Additional General Topics

• Amino Acid Hydrophobicity Scales
• Atom Types
• Attributes
• Attribute Assignment Files
• Automatic Styling (Smart Initial Display)
• BILD Format
• ChimeraX Advantages
• ChimeraX DICOM Reference
• ChimeraX Positions Format
• Clustal Conservation Groups
• Coloring by Model, Chain, Residue, Element
• DICOM Files
• Display Hierarchy
• EMDB Segmentation File Format (SFF)
• Fetch by ID
• IMOD Segmentation Files
• Introduction to PDB Format
• Markers and Links
• Model Information
• Mutation Scores Format
• Palettes
• Pseudobonds
• Select Contacts
• Select Sequence
• Sequence Coloring Format
• Similar Structures Format
• STORM Format
• Symbols for Image Annotation
• System Command-Line Options
• Target Specification in ChimeraX versus Chimera
• Trajectories, Model Series, Volume Series
• VDW Radii
• VTK Format

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UCSF Resource for Biocomputing, Visualization, and Informatics / November 2024