Guides
Wayfinders for our collections, tools, and servicesSoftware Licensed by the Science Library: Support and Resources
Download software, documentation, and support materials from PyMOL "incentive" content area
- PyMOL "Incentive" user area"PyMOL subscribers receive access to download software, documentation, installation instructions, and narrated screencasts through the PyMOL Incentive User Area." Please note that links for "incentive" content on the dokuwiki page all begin with https://pymol.org/dsc/
PyMOL support
Contents:
- Learn how to use PyMOL - start here
- Featured PyMOL tutorials on YouTube
- PyMOL "incentive" content for site-licensed users
- PyMOL support and resources - available to all
- Creating a molecular dynamics movie using PyMOL
- SARS-CoV-2 Structure (COVID-19 Coronavirus) plus PyMOL tutorial on how this movie was made
Learn how to use PyMOL - start here
- Practical PyMOL for beginners"Although PyMOL has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMOL interface and basic tasks without leaving the mouse behind."
- PyMOL quick reference for beginnersDownloaded to Google Drive with access limited to Stanford users.
- PyMOL quick reference for intermediate usersDownloaded to Google Drive with access limited to Stanford users.
- PyMOL cheat sheetReference card showing commands used in PyMOL.
- PyMOLWiki"PyMOLWiki includes tutorials, scripts, plugins, answers to frequently asked questions, and more. A user-maintained knowledge base, the PyMOLWiki is full of helpful information."
Featured PyMOL tutorials on YouTube
- PyMOL tutorials by PyMOL RossPyMOL tutorial 1: Introduction and using the GUI, PyMOL tutorial 2 : Making selections and using commands, PyMOL tutorial 3 : Publication Quality Images, PyMOL tutorial 4 : Making Movies, PyMOL tutorial 5 : Building and Manipulating, PyMOL tutorial 6 : FAQ - proximity selection, recording data, electron density, PyMOL Quickie - Electron Density, PyMOL Quickie - Making Mutations
- PyMOL tutorials by Molecular MemoryPyMOL: Active Sites in Minutes (Using only Sequence Info!), PyMOL: Build Your Own Sequences (for Learners & Instructors), PyMOL: Labels (That actually look good!), PyMOL: Working with Scenes (will save your butt!), PyMOL: Let's make a MOVIE!, PyMOL: Superimpose (& Amazing NMR Structures!), PyMOL Tutorial: Modeling the SARS-CoV-2 RBD Interactions with ACE (COVID-19 Coronavirus Proteins), and Where's My Dimer? Symmetry Mates in PyMOL.
PyMOL "incentive" content for site-licensed users
For "Incentive resources," please request registration information from the Science Library (see Request License Keys page for details). After filling out an online registration form, you will be sent a personalized link by email for accessing "incentive" content.
We have two accounts to the incentive area, one for each license agreement: (1) license expires December 31, 2024, and (2) license expires December 31, 2021. AxPyMOL software is only available in the incentive area that expires in 2021. Please see the Request license key page for instructions on how to register and get access to "incentive" content.
- PyMOL "Incentive" user area"PyMOL subscribers receive access to download software, documentation, installation instructions, and narrated screencasts through the PyMOL Incentive User Area." Please note that links for "incentive" content on the dokuwiki page all begin with https://pymol.org/dsc/
- PyMOL incentive product tutorialsTutorials available include: Introduction to PyMOL, Intermediate PyMOL, Moviemaking in PyMOL, and Molecular Editing and Small Molecule Cleanup,
PyMOL support and resources - available to all
- PyMOLWiki"PyMOLWiki includes tutorials, scripts, plugins, answers to frequently asked questions, and more. A user-maintained knowledge base, the PyMOLWiki is full of helpful information."
- PyMOL supportIncludes PyMOL installation instructions, supported operating systems and hardware, FAQs (Frequently Asked Questions), Known Issues, Citing PyMOL and AxPyMOL, plus professional support and community-sponsored resources.
- PyMOL dokuwiki"Legacy Documentation: This page contains a significant amount of legacy documentation, including outdated information and dead links. It's mostly retained for historical reference. The PyMOLWiki – which is maintained by the community and by Schrödinger – may contain more relevant and/or more up-to-date content." Please note that links for "incentive" content on the Dokuwiki page all begin with https://pymol.org/dsc/ and that access to this content is limited to site-licensed users.
Creating a molecular dynamics movie using PyMOL
Creating a Molecular Dynamics Movie in PyMOL (4:28 minutes, posted by SchrödingerTV on YouTube, November 18, 2020).
SARS-CoV-2 structure (COVID-19 coronavirus)
SARS-CoV-2 Structure (COVID-19 Coronavirus) (12:00 minutes, posted by Molecular Memory on YouTube, April 3, 2020.)
Description: "A structural exploration of the proteins produced by SARS-CoV-2."
PyMOL Tutorial: Modeling the SARS-CoV-2 RBD Interactions with ACE (COVID-19 Coronavirus Proteins). (25:01 minutes, posted by Molecular Memory on YouTube, April 21, 2020.)
Description: "A follow up PyMOL tutorial for my SARS-CoV-2 Structure. How I modeled the polar interactions between the spike protein RBD and ACE before the paper was published (and a follow up interaction now that the paper is published!)."
