Analysing an active
Building a functionnal unit
from a monomer
Electron Density Maps
Fitting Residues into
31 March 98
maps : fatty acid binding protein
To complete this tutorial,
you will need to download some material (coordinates and
electron density map of the lysozyme). This data set has
kindly been made available by Dr. Jim Thompson, Dr. Nate
Winter and Prof. Len Banaszak
- material for Macintosh (.hqx 855 Kb)
- material for PC (.zip 553 Kb)
Stereo detail of a part of the fatty acid binding
protein. Rendering with POV-Ray.
Step by Step
- First of all, if you are using a Macintosh, make sure
that Swiss-PdbViewer has at least 6000Kb of free memory
to run (click on the icon, press Command I, and adjust
the memory allocated to the program). Then launch it.
- Open the pdb file lfabp .pdb.
- Then, verify that the checkbox "center upon loading"
of the "General preference" is not checked. If it
was checked, uncheck it, close the protein and reload
- Center the view by hitting the "=" key of the
numerical keypad right mouse button on the PC), and
enable the "Slab" item of the Display Menu.
- Click on the first button at the top left of the main
window and set the "slab depth" to 8Å in order to
limit the quantity of information displayed on screen at
the same time.
- Select the Open DN6 Map from the file menu and load
the file "lfabp.dn6".
A dialog will appear. The upper part provides some
information about the unit cell size: the length along
its axis, and the angle between the axis. Note that the
axis are not necessarily orthogonal. It all depends on
the crystal symmetry. In this case, there is an angle of
120° between axis x and y.
Below are some information on the number of sections
available in the map. As a whole edm is pretty heavy to
handle, it is advised to display only a subpart of it. In
our case, we will display only from sections 50, 20 and
40 (along X,Y and Z respectively) to sections 80, 50 and
The last part of the dialog let you decide what will
be the cutoff density for the contouring, i.e.
decide what are the limit between a dense zone and a zone
with low edm.
Type 2.5 in the field and accept these settings.
Amino-acids belonging to the antiparalell strand 99-113
are perfectly fitted within the electron density map.
What you see is in fact the final stage of the process.
During initial stages of the resolution of a protein, edm
are much more messy. Hold down the shift key while
clicking and moving the mouse toward you to move the slab
toward you. Some new parts of the protein will be
revealed, all of which are not contoured. Remember that
only a subpart of the edm was selected to be displayed.
Play a little with the protein; look at the anti parallel
b-stands, and so on.
- Now go to the control Panel and click on the Asp106
while holding down the control key (shift Control for
PC). This will automatically center its alpha carbon in
the view. Zoom in. Note that the sidechain is not buried
into the edm. It means that the location of the carboxyl
group is not very well defined in space. As a matter of
fact, sidechains of surface residues tend to be more
flexible and therefore do not diffract very well.
- Go back to the edm preferences dialog, and enable the
second contour with a 1.5 sigma value. Click on the
dotted checkbox, and accept the settings. A second
contour, englobing more parts of the structure, among
those the CG of Asp106 appears with an other colour. By
decreasing the sigma value, you contour parts of the map
that have a smaller electron density than when you use a
- Go back to the same dialog by hitting command+Y
(control+Y for the PC), disable the display of the second
contour and enable the dotted checkbox of the first
contour. The display will now look like a cloud of dots,
and the amino-acids appear more clearly within the
density (this mode will be useful until I add a Z-buffer
and also maybe a color-distance fading feature).
As you have noticed, only the part of the edm you have
selected to be displayed are actually shown. If you want
to inspect all amino-acids one by one to see how well
they fit into the edm, it would be useful to display only
subpart of the edm corresponding to the residue you
currently closely inspecting. Well, this is possible.
- Bring back the edm dialog and enable the radio button
entitled "Display around CB". By default, only parts of
the edm lying within 5Å of the carbon beta of the
currently centred residue (Ion our case Asp106) will be
displayed in each direction along the unit cell axis.
- Center the view on the next residue (simply hit the
right arrow key) and a new portion of the edm will be
displayed. Navigate down along the peptide to look at the
edm, and stop on the residue Asp87. Here again, you can
see that only no density is displayed around the
sidechain. It is therefore very useful to be able to
change the sigma value used for the contouring. This can
be done without using the edm preference dialog: simply
hit the down arrow key and the sigma contouring value
will be decreased by 0.1. Hit the down arrow key 10 times
more and look how the edm displayed increasingly covers
the atoms. (note: typing the down arrow key while
maintaining the shift key down will decrease the sigma
value for the second contouring value).
- Colour the protein by B-factor. Look at how the
sidechain of the Asp87 appears reddish. This means indeed
that the electron density is badly defined in this
- Now Bring back the edm dialog and enable the coarse
contouring along the Z axis. The contouring will be less
fine bet the display should appear slightly less
cluttered and faster.Play a little with the coarse
checkboxes to look at the effect. Usually, working with
one or two axis coarsely contoured allows a good
rendering speed without noticeably affecting the display
- Click on the small text icon located at the right of
the earth icon. in the main window. The text file will
the coordinates of the currently active pdb file are
displayed. Scroll down to the residue Asp87, and look at
the B-factor of atoms OD1 and OD2 (last column containing
digits). It is 85.39 and 84.53, which is very high.
Colouring a protein by B-factor allows to immediately
identify regions that are more accurately fixed in space
than other (usually the core of the protein).
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