PyMOL
The material for this series of workshops is provided as a printed workbook of 173 pages loaned during classes. PyMOL workshops are currently split into 3 successive sessions.
Materials below is a slide hand-out (PDF format) and in-class set-up and summary (as live Jupyter notebook.)
At the bottom of this page, check out the video tutorials playlists from YouTube.
PyMOL Tutorial books
See also post PyMOL Tutorial Books Released (June 20, 2019)
The Biochem 660 PyMOL tutorial book has been split in 4 PDFs for easier read and download:
- Book 1: Molecular Graphics Essentials (Summary of methods to acquire 3D data; file formats)
- Book 2: PyMOL part 1 (Graphical representations and atom selection, electrostatic potentials, side-chain mutations, 3D overlays, …)
- Book 3: PyMOL part 2 (scripts, animations and movies, multimeric structures, morphing)
- Book 4: PyMOL part 3 (Electron Density Maps)
PyMOL Resources
On-line hand-outs:
Added note: Parts 1-3 of the hand outs correspond altogether to books 2 and 3 above (PyMOL parts 1 and 2)
PyMOL_part 1 (of 3)
- Slides hand out part 1 (PDF, color, 6 slides per page) (last updated – September 11, 2018)
- Short hand out part 1 (rendered ipython jupyter notebook)
PyMOL_part 2 (of 3)
- Slides hand out part 2 (PDF, color, 6 slides per page)
- Short hand out Part 2 (rendered ipython jupyter notebook)
PyMOL_part 3 (of 3)
- Slides hand out part 3 (PDF, color, 6 slides per page)
- Short hand out Part 3 (rendered ipython jupyter notebook)
(PYMOL sections last updated: September | October 2017)
Video Tutorials (External)
Playlist from Channel “Molecular Memory“
Playlist from “Swanson Does Science“