Workshop: Visualizing 3D structures with Pymol.
- An introduction to using Pymol to vizualize 3D PDB structures
- Duration: 90 minutes
- 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.
- Advanced topics:
- Electrostaic surface coloring
- High quality rendering
Required software and resources
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:
- Brief description of protein function and the selection of PDB structutes (at least two).
- Analysis of PDB files content, asymmetric unit, ligands, engineered components.
- Bioassembly and relation of PDB contents to the biologically active assembly.
- Visualization of the biologically relevant structure (clearly show ligands if present, any functionally relevant components).
- Analysis of PDB quality and your summary. What regions have good/poor quality?
- B-factor visualization (color scale should be given).
- Occupancy analysis
- Identify any potential NQ-flips.
- Analyze and visualize electron density together with the structure, see if any problems can be seen.
- Electorstatic surface analysis
- Make figures showing changes in conformation by structural superposition. Make a morphing video if possible.
- Identify and visualize key residues important for ligand binding.
- Describe any problems encountered
Suggested problem sets
Each student should take a unique problem.
- Make analysis of heaemoglobin and Oxy-deoxy transition (see https://pdb101.rcsb.org/motm/41)
- Make analysis of opening and closing of potassium ion channels (see https://pdb101.rcsb.org/motm/41)
- Analyze nucleosomal DNA unwrapping (1KX5 - wrapped nucleosome, 6ESH - unwrapped)
- Make analysis of Spike-protein (see https://pdb101.rcsb.org/motm/246)
- Any molecule of the month that has more than one conformational state (https://pdb101.rcsb.org/motm/motm-by-date)
- Consult with the seminar protocol/recording
- Try to Google, and see Pymol Wiki
- Ask questions in Slack