This page: www.rbvi.ucsf.edu/chimera/data/tutorials/systems/
← BP205A syllabus

• presentation/demo – Elaine
  • [outline and sample data]
  
  
• Q & A – Elaine & Eric

• Chimera homepage (downloads, etc.)
  
  
• User's Guide (also included in the download)
  • Sequences and Structures tutorial
  • Multalign Viewer
    • alignment header file format
  • Attributes tutorial
    • attribute file format
  • Chimera commands index
  • Tips on preparing images
  • Making movies
  • Intro to PDB format
  
  
• Movie-making tutorial (2012)

• Online sources of sequence alignments
  
  
• AL2CO conservation calculations implemented in Chimera (see Multalign Viewer Header preferences):

  AL2CO: calculation of positional conservation in a protein sequence alignment. Pei J, Grishin NV. Bioinformatics. 2001 Aug;17(8):700-12.

• A good review on per-column measures of conservation (several of which are implemented in the AACon web service connected to Jalview):

  Scoring residue conservation. Valdar WS. Proteins. 2002 Aug 1;48(2):227-41.
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