Analyzing and Comparing Structures with UCSF Chimera

Analyzing and Comparing Structures
with UCSF Chimera

Demonstration (~20 mins):
- general concepts and tips for using Chimera
- preview of some of the tools you will be using
- OK (preferable?) to watch rather than trying to follow along; if you do try things, close session or quit/restart before starting the tutorial
Hands-on tutorial:
- Structure Analysis and Comparison (~45 minutes)
Optional tutorials (available from Help menu):
- Attributes (~20 minutes)
- Trajectory and Ensemble Analysis (~35 minutes)
- The Model Panel and Ensembles (~20 minutes)

Turning Data into Information

molecular graphics as an analysis tool
visual presentation of information carried in atomic coordinates
mapping non-coordinate information onto graphics

Demonstration Outline

General concepts, basic structure analysis:

customizing tool startup and icons with Preferences
zone selection
measuring a distance
identifying hydrogen bonds (FindHBond)
commands and atom specification symbols
command help, Help buttons, Help menu
documentation is local (included in download) and searchable

Structure comparison:

superimposing structures with MatchMaker
morphing between different conformations
viewing and recording a morph trajectory with MD Movie

Attributes (atom and residue property values):

showing B-factor with colors using Render by Attribute
showing amino acid hydrophobicity with “worms”
attributes can be used in commands
users can define custom attributes in a simple text format
various operations in Chimera also create attributes (surface area, conservation in an alignment, etc.)