Structure analysis:
- hydrogen bonds and contacts
- amino acid sidechain conformations
- properties (B-factor, hydrophobicity, etc.)
Comparison:
- superimposing structures
- morphing between structures
An ensemble = multiple sets of coordinates for the same set of atoms
- Demonstration (~25 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 copy my actions;
if you do try things, close session before starting tutorials
- Hands-on tutorials:
- Structure Analysis and Comparison tutorial
- Trajectory and Ensemble Analysis tutorial (optional)
- ensemble treated as a time series or trajectory
- The Model Panel and Ensembles tutorial (optional)
- ensemble treated as multiple models that can be viewed together
All demonstration and tutorial data files are in the
chimera-analysis folder on the Desktop.
If you don't have that folder, download it from
www.cgl.ucsf.edu/chimera/data/tutorials/library/class.html
The tutorials and associated data are also included with Chimera and
can be accessed from the Help menu, so you can use them at any time
(independent of this class).
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