Software, Data, Other Resources
3D Structure Viewers
We predominantly use PyMOL for our protein 3D structure teaching
It has the disadvantage that it is not browser-based i.e. that it
requires users to install the PyMOL software themselves, locally,
directly on their own computer - however, for us, the above advantages
of using the software outweigh this disadvantage.
- PyMOL is (relatively) easy to learn (at least for basic view
- user-specified views of 3D structures can be easily created by
trainers, and loaded into PyMOL by trainees, to demonstrate particular
features of protein structure etc.
- we use it in our own work - so we are reasonably well-placed to
provide help and advice for trainees using the tool for the first time
- release 0.99 is free, and in our experience easy to install on a
range of different systems
Note, however, that there are many other software packages available
the specialise in visualising 3D protein (and other biomolecule)
Here are some sites describing more complete lists of 3D structure
3D Structure Data Formats
Most biological 3D structure viewers can read in data in the PDB format
- here is a description of
Most 3D structure viewers are also able to save structural data in a
format specific for that software - this typically contains not just
the 3D coordiates and other information contained in the initial
(typically PDB-format) file, but also the information required to
specficy the representation of the protein. In PyMOL, such files are
known as "Session Files".
Obtaining 3D Protein Structure Data
PDB format 3D structure files are available from several different
internet resources including:
Recently-released version of PyMOL must be bought from DeLano Scientific Limited.
However, the no-longer-supported release 0.99 is free for all to download and use for Windows,
Macintosh, and Linux.
Information and Tutorials on PyMOL
There are several sources of information on PyMOL on the Internet
Note that the instructions and screen-shots shown below are for the
Macintosh version 0.99 of PyMOL - they will be similar, with hopefully
only slight differences, on the Windows and Linux versions of the
To obtain the full functionality of this software, you will need a
three-button mouse (e.g. for Macintosh you could be using a "Mighty
Loading a Structure
There are several ways to load a structure file into PyMOL
- it is possible to set up your computer so that simply clicking on
the icon representing the structure file (typically with the ending
.pdb or pse), the file will open in PyMOL
- it may also be possible to just drag-and-drop the structure file
onto the PyMOL main-window
- something that should be standard and work on all operating
systems is to go via the File->Open on the Menu-Bar. Additionally,
this method can be used to add additional structures from other files
to the same viewing space
Changing the Viewpoint
To change the viewpoint, simply place the mouse pointer somewhere in
the structure viewer window, click and hold down one of the three mouse
buttons, and then move the mouse. Depending on which mouse button is
held, the viewpoint will either rotate (left button), translate (middle
button), or zoom (right button).
It is possible to set up PyMOL so that different mouse buttons (and
different combinations of mouse buttons with keys such as shift and
control) have different effects on the viewpoint - however we will
stick with using the default settings.
When preparing figures for printing, we usually choose to change the
background colour from black to white to save ink/toner in our printers.
To change the background colour, choose Display->Background->White
Filling the Viewer
with the Entire Structure
Sometimes we can get in a bit of a mess when changing the viewpoint -
Zooming in so that the structure is so far that we can no
longer orient ourselves
(which is based on this PyMOL
Or zooming out so much that we can no longer
find the structure within the structure viewing window
(which is based on this PyMOL
To rescue this situation, just click on the "Zoom" button - this should
return to a viewpoint where the entire structure more-or-less fills the
structure viewing window.
Viewing the Protein
Once you have loaded a structure file into PyMOL you may want to also
see the sequence of any peptides (and information about the names of
residues from other non-peptide molecules macromolecules) of the chains
included in the structure file.
To do this, you need to switch on the "Sequence On" option, accessed
via the "Display" Menu-Bar menu
This will then display the sequence of the chains as shown below - with
the sequence residues coloured the same as the corresponding regions of
Regions of the Structure
To select (and thus highlight/change colour/change representation of)
amino acid residues in the sequence, simply select the residues you
want to highlight using the left mouse button - or to select several at
the same time, just drag along the sequence while holding the left
The selected sequence residues will be highlighted in the sequence - at
the same time, the regions of the structure corresponding to these
residues will also be highlighted by adding purple dots to the selected
Residues can also be selected by left-clicking on them directly in the
stucture viewer window (and, most powerfully, by using the "select"
command at the PyMOL prompt - but we won't cover that here.)
Operating on Selections
Once a selection is created, you can change aspects of the way it is
displayed, and use it as the basis of a range of different operations
e.g. you could use it to create a further selection that contains all
atoms/residues within a given distance of the initial selection, you
could predict polar contacts within the region, etc.
To operate on the selection using the PyMOL graphical interface, we
work with the selection list on the right side of the interface window
- for example, in the image shown below, there are four different
selections listed, with names:
You'll notice that each selection has a set of 5 buttons associated
with it - these are:
A - "action"
By clicking on these buttons, menus of actions that can be applied to
the selection are shown - a different menu for each of the 5 different
buttons. For example, in the image below, the "C" (colour) button has
been clicked, producing the colour menu (from which a further "Magenta"
menu has been revealed by selecting one of the elements from the colour
S - "show"
H - "hide"
L - "label"
C - "colour"
"all" and "sele" selections
If there is any data loaded into PyMOL, then there will be at least one
selection in the list - the "all" selection. This selection includes
all the atoms currently loaded into PyMOL, and allows the user to make
If there are any selected residues/atoms etc. within the structure, and
the selections have not been deliberately renamed, then there will be a
second selection on the list, "sele", which is associated with the
currently selected set of atoms/residues etc.
"C" - Changing the
Colour of a Selection
To change the colour of the selection, click with the left mouse button
over the "C" box associated with the selection
Then choose the colour you want for the selection - below we choose
magenta as the new colour
The selected amino-acid residues, both in the sequece viewer, and in
the structure, have changed colour to magenta
Alternatively, you can choose to colour different regions of the
structure using a set of rules - these include:
- "by element" - useful when you're interested in the details of
the chemistry of a particular region of the protein - the default is:
- carbon - green
- oxygen - red
- nitrogen - blue
- hydrogen - white
- sulphur - orange
- "by chain" - useful to visualise the quaterunary structure of the
- each of the different chains described in the PDB file is
assigned (automatically) a different colour
- "by ss" (i.e. "by secondary structure") - useful to get an
overview of the tertiary structure of the protein - the default is:
- alpha helix - red
- beta strand - yellow
- loop - green
"H" - hiding
regions of the selection
To make particular features of a structure easier to visualise, we
often want to hide parts of the representation - and to do this we use
the "H" hide button.
For example, we often begin a session by hiding everything from the
"all" selection so that we can build up exactly the representation we
In the "H" menu we get the choice to hide:
- everything - all atoms bonds etc. associated with that
- lines/sticks/ribbon/cartoon - these are four different
ways of representing polypeptide chains. Several of them can be used at
the same time, so you can hide the "sphere" representation and find
that underneath it the "stick" representation is still in place
- side chain/main chain - it's possible to hide either only
the main chain or only the side chain atoms using these options
Changing the Origin of Rotation
Select a region of interest (as described above),
on the selection, and choose "Origin" from the menu that
Alternatively, select the residue, and use the "A" (action) menu to
choose the selection as the new origin of rotation - select "origin"
from the action menu.
To align to structures/regions of structures with each other, left
click with the mouse over the "A" ("Action") button for the object or
selection you want to align
Here you choose the "Align" action, then usually "to selection"
(although try "to molecule" if this option doesn't work), and then
select the name of the selection you want to align to
This will carry out a (rather simple and not very accurate) alignment
of the structure of the two selections - as seen below
Saving a PyMOL
Sometimes you will want to save the image you have obtained in the
PyMOL view screen as a separate image file. To do this, use the
Author: Aidan Budd