Molecular Graphics and Protein Visualization: Pymol
with web browser
molecular graphics application
tutorial can be found here:
of this web tutorial originate from the Pymol Manual/tutorial, which is
hardware accelerated graphics card is desirable (anything that is decent
for modern video games)
- A three
button scroll mouse is also helpful
are a whole lot of molecular graphics programs available. Many of them are
freely available. Pymol is one of the most powerful and is capable of
publication quality images and animations.
is a shareware program. Please see the web site for information on
will be using PCs running linux for this exercise, but you should be able
to do all of the same things on windows or mac osx.
setup on the workstations
as user=xxxx password=yyyy (will be provided during class)
up a terminal window and create a working directory for yourself using
the unix ‘mkdir’ command.
the structure files you will use to this directory
to locate structures. Open up a web browser, such as firefox.
Protein Data Bank (RCSB=Research Collaboratory for Structural
you go to RCSB, you might select the beta site if it is available:
you know what you are after, you can search for structures in the
database using the pdb search or advanced search functions
data is also linked to other online databases, such as at NCBI, http://www.ncbi.nlm.nih.gov/
way to find interested molecules is via the “Molecule of the Month”:
curated gallery of selected structures. Includes some background information
about the protein. It also shows some sample images
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
a text editor to view and manipulate the coordinate file
the edited coordinate file into Pymol
Molecule I: HIV
Molecule II: EcoRI
Molecule IV. PKA (Protein Kinase A)
Electron density server:
save map as xplor/CNS format
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.
2fofc.xplor,map1 # type inferred from the
2fofc.map,map1,1,xplor # type
Action -> Mesh @ level 1.0
Action -> level 0.5
There are a number of very good tutorials in the pymol
Spend any remaining time going over the tutorial:
All of the files for this tutorial are here: