Recitation 2: Pymol

Basic (✓)

• If you have not yet installed open-source pymol on your local machine:

  • Create a new conda environment
  • Activate the environment
  • conda install conda-forge::pymol-open-source

• Follow along with brief introductory pymol demo

• Generate high-quality figures (must be ray traced) of profilin 1 showing any differences between the WT and mutant protein:

  • Wild-type profilin-1 PDB: 4X1L
  • M114T profilin-1 PDB: 4X25

• Have a TA/instructor check your work

• Upload your figure(s) with a caption and your name to GradeScope.

Extra (✓+)

• Visualize the electron density map of 7m6q (need to get from EMDB)
• Identify evidence of a chloride atom that is not in the pdb
• Comment on anything else you observe

Notes:

• The Protein Data Bank (PDB) is a global archive of structural coordinates https://www.rcsb.org/

• Pymol has a great wiki for learning how to use commands: https://pymolwiki.org/index.php/Main_Page

• Some useful commands:

  • Color: https://pymolwiki.org/index.php/Color
  • Show: https://pymolwiki.org/index.php/Show
  • Align: https://pymolwiki.org/index.php/Align
  • Super: https://pymolwiki.org/index.php/Super
  • Distance: https://pymolwiki.org/index.php/Distance
  • Ray: https://pymolwiki.org/index.php/Ray
  • Fetch: https://pymolwiki.org/index.php/Fetch
  • Load: https://pymolwiki.org/index.php/Load

• Pymol also supports python scripting - https://pymolwiki.org/index.php/Simple_Scripting