mm_hse_2023

Workshop 3. Visualization of 3D structures in Chimera.

Workshop plan

• An introduction to using Chimera to vizualize and manipulate 3D PDB structures
• Chimera user interface orientation
• Download and open PDB structure
• Rotating, translating, setting clipping planes, projection type, centering (actions) etc.
• Moving structure (actions)
• Making selections (by chains, residues, sequence, etc.)
• Structure visualization modes (atoms, ribbon, surface)
• Coloring (by attribute)
• Combining structures
• Structure and sequence alignment
• Building and changing structures (angles, bonds, rotamers)

Required software and resources

• UCSF Chimera
• 3-button mouse

Learning resources

• Chimera User’s Guide

Assignments

A set of PDB structures of a macromolecular complex in different conformations will be suggested for analysis. The assignment report should include section detailing the following:

1. Visualize a molecule with labeled and differently colored positive, negative or aromatic amino acids and semitransparent surface.
2. Identify any clashes and fix them rotating amino acids angles.
3. Make structure and sequence alignment of chosen molecule with any of its homologs, color matching domains.
4. Choose any segment of sequence alignment and introduce amino acid substitutions to make both chains completely matching.
5. Make conservation analysis of aligned structures.
6. Describe any problems encountered *. Write a script/demo for the task 1 with adding molecule name in the right upper corner and 360 degree rotating around every axis before and after changing the model.

Suggested problem sets

Each student should take a unique structure.

1. Any molecule of the month that has at least one homolog (https://pdb101.rcsb.org/motm/motm-by-date).
2. Any protein structure that has at least one homolog.

Troubleshooting

• Consult with the workshop protocol/recording
• Try to Google, and see Chimera User’s Guide
• Ask questions in Telegram