PyMOL part 2 (of 3)

Biochemistry laboratories - 201

Jean-Yves Sgro

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Note: To see as slides click on gift icon at the top right. To revert back to page view click on book icon when on the first slide.


  • check your name on the attendees list
  • choose an iMac (or use your laptop)
  • login with your UW Net ID

Today summary slides

Finding PyMOL

  • Click on the "Finder" at the bottom right of the "Dock" on the bottom of the screen.
  • This will open a new window.
  • On the left click on "Applications"
  • In the alphabetical list choose "MacPyMOL" or "" and double click. This will open PyMOL on your screen.

PyMOL book: section for part 2 (of 3)

  • start on page 79
  • end on page 106

This book is a loaner with a number marked on it.
Please do not take with you.

Today's menu

  • Clipping planes and surfaces (p 79)
  • Distances and Labels (p 82) - Wizard
  • Extract and modify ligand (p 88)
  • Display H-bonds (p 91)
  • Electrostatic potential (p 93)
  • Side chain mutation (p 98) - Wizard
  • Automatic 3D superimposition (p 102)
  • Model building (alpha helix; p 106)

To get your own PyMOL workbook in PDF format:

  • fill-in the one page 1 page survey "evaluation" form for this class
  • BONUS: Complete PDF of PyMOL workbook used in class

The evaluation is anonymous, click (or type) either link below:

[If necessary survey will be unlocked when workshop occurs]