Guide to Pymol

Download and Install PyMol

1. Download and install pymol from http://delsci.com/rel/. Binaries for OS X and
Windows are available as is the source.
Interactive usage
1. Launch pymol. The pymol viewer consists of a couple of windows. The grey
window in the top third gives text output (such as the atoms and residues
selected) and error messages. The black window below displays the molecule.
There are two modes of interacting with pymol : using the menu (located on top
and the right sides) and using the command line (located at the bottom of the
grey and the black windows).

2. We will now use pymol to load a pdb file and color some residues.
a. Load the pdb file

b. Switch to space-filling representation.

> show sphere

c. Select the water molecule.

> select waters, resn HOH
This also creates an entry on the right tab which can be used to operate
on the water molecules.

d. Remove the water molecule.

> remove waters
You can also remove the water molecule by clicking on the option H
on the tab labeled waters (S for select, A for actions, H for hide, L for label)
and clicking on hide everything.

e. Color the rest of the protein white.

> color white, all

f.

Color the activesite (residues 5 and 6) red.

> select activesite, resid 5+6
> color red, activesite

g. Now rotate the protein around its vertical axis to view the active site.

h. Save your work as a pymol session (this will allow you to resume where
you left off).
> save 1BNA.pse
i.

You can also save the image alone.

> save 1BNA-activesite-1.png
> rotate y, 180
> save 1BNA-activesite-2.png

j.

Exit pymol.
> quit

k. To resume, restart pymol and type > load 1BNA.pse from the
command-line (or open the file using the menu >file>open).
PyMol scripts
1. The commands used above can be placed in a script which can then be invoked
to repeat these actions. For instance, type the following commands on each line
of a file called color-activesite.pml
load 1BNA.pdb
show spheres
select waters, resn HOH

2. From the command-line, run the script by typing

$ pymol color-activesite.pml
Objects in PyMol
1. To manipulate the structure, PyMol allows you to create objects i.e., subsets of
atoms. These objects are created using the select command. For example, the
command select waters, resn HOH creates an object named water
consisting of all residues in the PDB file whose name is HOH. Similarly, the
command select activesite, resid 5+6 creates an object named
activesite consisting of residues 5 and 6 (in all the chains of this PDB file). After
an object has been created, an entry for this object appears on the right tab.
2. The object can then be manipulated separately. For example, the command
color red, activesite colors read only the atoms that belong to the
activesite object created above.
3. Some more manipulations on objects

a. Objects can be selected using more complicated selection criteria. Heres

an example on 12as.pdb.
i. Select residue 46 in chain A : > select activesite,
chain A and resid 46
ii. Select all water molecules within 10 angstroms of residue 46 in
chain A:
> select epitope, (( chain A and resid 46 )
around 10) and resn HOH)
iii. Other logical operators can be used for selection (see
http://pymolwiki.org/index.php/Selection_Algebra)
iv. To deselect an object, use: deselect epitope.
b. These objects can be manipulated in many ways, e.g.,
i. Change the representation to space-fill, stick or surface:
> show [sphere or sticks or surface], epitope

ii. Zoom in to the object

> zoom epitope

Creating high-quality images

1. To create the final high-quality version of the image, use these commands:
> ray 2400, 2400
> save figure.png