mm_2024

Workshop: Visualizing 3D structures with Pymol.

Description

• An introduction to using Pymol to vizualize 3D PDB structures
• Duration: 90 minutes
• Objectives:
  • Pymol user interface orientation
  • Download and open PDB structure
  • Rotating, translating, setting clipping planes, projection type, centering (actions) etc.
  • Structure visualization modes (presets, lines, sticks, spheres)
  • Making selections (by chains, sequence, etc.).
  • Pymol selection language
  • Molecular surfaces
  • Structure alignment
  • Manipulating, moving structure (actions)
  • Adding H-atoms.
  • Calculating charge
  • Loading biounit, combining models, saving pdb-files.
  • Morphing, visualizing conformational transitions.
  • Coloring structure by parameters (B-factors)
  • Comparing PDB with electron density.
  • Scripting
• Advanced topics:
  • Electrostaic surface coloring
  • High quality rendering

Required software and resources

• Pymol, installation instructions
• 3-button mouse

Learning resources

• Pymol Wiki https://pymolwiki.org/index.php/Main_Page

Workshop protocol

protocol.pdf

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. Brief description of protein function and the selection of PDB structutes (at least two).
2. Analysis of PDB files content, asymmetric unit, ligands, engineered components.
3. Bioassembly and relation of PDB contents to the biologically active assembly.
4. Visualization of the biologically relevant structure (clearly show ligands if present, any functionally relevant components).
5. Analysis of PDB quality and your summary. What regions have good/poor quality?
6. B-factor visualization (color scale should be given).
7. Occupancy analysis
8. Identify any potential NQ-flips.
9. Analyze and visualize electron density together with the structure, see if any problems can be seen.
10. Electorstatic surface analysis
11. Make figures showing changes in conformation by structural superposition. Make a morphing video if possible.
12. Identify and visualize key residues important for ligand binding.
13. Describe any problems encountered

Suggested problem sets

Each student should take a unique problem.

1. Make analysis of heaemoglobin and Oxy-deoxy transition (see https://pdb101.rcsb.org/motm/41)
2. Make analysis of opening and closing of potassium ion channels (see https://pdb101.rcsb.org/motm/41)
3. Analyze nucleosomal DNA unwrapping (1KX5 - wrapped nucleosome, 6ESH - unwrapped)
4. Make analysis of Spike-protein (see https://pdb101.rcsb.org/motm/246)
5. Any molecule of the month that has more than one conformational state (https://pdb101.rcsb.org/motm/motm-by-date)

Troubleshooting

• Consult with the seminar protocol/recording
• Try to Google, and see Pymol Wiki
• Ask questions in Slack