"

I.D. Getting Started with PyMOL

Roderico Acevedo and Kristen Procko

Overview: This chapter presents the PyMOL interface, guides the user to load a structure, and introduces trackpad and mouse controls.

Outcome: The user will be able to load a file in PyMOL, perform basic manipulations (zoom, rotate, and center), save a PNG file and save all work (for PyMOL, this is a session file).

Time to complete: 5–10 minutes

Modeling Skills

  • Load a structure into the modeling program.
  • Perform basic structure manipulations (e.g., zoom and rotate) with a trackpad or mouse.

About the Model

PDB ID: 3fgu

Protein: Catalytic complex of Human Glucokinase

Activity:  One isoform of the enzyme that phosphorylates glucose in the first step of glycolysis

Description:  Single chain, with four bound ions and molecules. Potassium ion (K+) is from the crystallization medium and non-essential for biological function. Bound catalytic magnesium (Mg2+). Bound substrate: beta-D-glucose, and bound substrate analog phosphoaminophosphonic acid-adenylate ester (ANP). ANP is a non-hydrolyzable analog of ATP, thus this structure captures a similar view to the catalytic complex (enzyme-substrate complex).

The PyMOL User Interface

Throughout these tutorials, we will refer to the following parts of the interface:

PyMOL interface on a computer screen, showcasing various plant parts and emphasizing different menus and buttons. Labeled components include: dropdown menu, structure viewer, command line, building buttons, names/ object panel, controls.
Figure 1: Shows the PyMOL screen and highlights different menus and buttons.

Steps

  1. Open PyMOL by double-clicking on the application
  2. In the top command line, type: fetch 3fgu, type=pdb1

Note: The default render is ribbon (cartoon) with black background, and small molecules shown as sticks or spheres. 

 

  1. Now, familiarize yourself with basic structure manipulation using the guide below. Based on your specific trackpad or mouse, these may vary slightly. Play around to see how yours works.
    • rotate: click and drag (mouse: left click and drag)
    • zoom: pinch and spread (mouse: right click and drag)
    • translate: ctrl+ click and drag (mouse: command + left click and drag); mac: command button
    • re-center: right hand names/object panel → A button → orient or center
      • another option to re-center, once a selection is made, is to right-click and choose “center(vis)” in the popup menu
  2. Position and zoom the structure as desired.
  3. Save the file in two ways:
    • Save a png image
      • In Building buttons panel, click on Draw/Ray.
      • elect either “Draw(fast)” or “Ray(slow)”. Ray has higher quality rendering, but it is slower.
    • Save a PyMOL session file
      • Go to File –> Save session. Type a filename in the box and click “Save.”
    • Reopen a PyMOL session file
      • In the dropdown menu, click: File → Open
      • In the popup menu, select the PyMOL session file (.pse)

Note: The option to “Draw(fast) or “Ray(slow)” will be remembered for the rest of the session. It will not appear again unless the session is restarted.

 

      • Click “Save Image to File” or “Copy Image to Clipboard”.
      • If “Save Image to File” is chosen a pop-up box will appear and allow you to type a filename and click “Save.”

Note: An alternative way to save a .png file is by using the dropdown menu. In the dropdown menu, click: File → Export Image As → PNG. This will bring up a popup box that will allow you to select between the following options: capture current display (screenshot, includes all PyMOL windows), draw antialiased OpenGL image (fast), and ray trace with opaque or transparent background (slow). Select an option and click: Save png as… to bring up the save popup window.

 

Click here to go to Chapter II: Alternative Renderings

License

Seeing the Invisible: Learning to Teach with Biomolecular Visualization Copyright © by The BioMolViz Working Group. All Rights Reserved.

Share This Book