Molecular Graphics and Protein Visualization: Pymol




  1. Computer with web browser
  2. Pymol molecular graphics application
  3. UM site-license:
  4. This tutorial can be found here:
  5. Portions of this web tutorial originate from the Pymol Manual/tutorial, which is posted here:




Experimental Procedure

  1. Get setup on the workstations
    1. Login as user=xxxx password=yyyy (will be provided during class)
    2. Open up a terminal window and create a working directory for yourself using the unix ‘mkdir’ command.

                                               i.     mkdir your-name

                                             ii.     Download the structure files you will use to this directory

  1. Propare to locate structures. Open up a web browser, such as firefox.
    1. RCSB-The Protein Data Bank (RCSB=Research Collaboratory for Structural Bioinformatics)

                                               i.     Go to

                                             ii.     When you go to RCSB, you might select the beta site if it is available:


    1. If you know what you are after, you can search for structures in the database using the pdb search or advanced search functions

                                               i.     The data is also linked to other online databases, such as at NCBI,

    1. Another way to find interested molecules is via the “Molecule of the Month”:

                                               i.     A curated gallery of selected structures. Includes some background information about the protein. It also shows some sample images


    1. Some specific examples of protein molecules are found below. During the course of this lab you will learn how to:

                                               i.      Download the atomic coordinates for each macromolecule

                                             ii.     Use a text editor to view and manipulate the coordinate file

                                            iii.     Load the edited coordinate file into Pymol

                                            iv.     Generate different

    1. The exercises:

                                               i.     HIV Protease

                                             ii.     EcoRI Endonuclease

                                            iii.     DNA polymerase



Molecule I: HIV Protease

Molecule II: EcoRI Endonuclease

Molecule III: DNA Polymerase


Molecule IV. PKA (Protein Kinase A)



Electron Density


Electron density server:

save map as xplor/CNS format


gzip –d

mv 2f4j.cns 2f4j_2fofc.xplor


Load pdb file into pymol


select display (i.e. sticks)


Load map into pymol.

Open -> 2f4j_2fofc.xplor


PyMOL expects XPLOR/CNS map files to have a ".xplor" extension. This requirement can be avoided by supplying an explicit type of "xplor" to the "load" command.


   load 2fofc.xplor,map1        # type inferred from the extension

   load,map1,1,xplor  # type explicitly provided


Display mesh:

Action -> Mesh @ level 1.0

Action -> level 0.5



There are a number of very good tutorials in the pymol manual


Spend any remaining time going over the tutorial:


All of the files for this tutorial are here: