Building Crystallographic Symmetries
In this example, we will learn how to
"populate" a unit cell by building the Crystal
Symmetries, and detect a water molecule that would not be
present in the crystal.
Step by Step
Display the "EDM preferences" dialog, and check the "Draw
Unit Cell Box".
Display the "Loading Preferences Dialog, and make sure
that the "Ignore Solvent" box is not checked, and
that the "Show Solvent (if loaded)" box is checked.
Now, open the pdb file 6PTI_bad (provided with the
tutorial package), scroll down
the Control Panel and locate the group HOH999. This is a
water molecule that I have added to the file for the sake of
the demonstration. Although this water molecule can make
good H-bond contacts, it cannot be there in the crystal.
Why? Let's examine this.
Use the "Build Crystallographic symmetry" of the tool
menu. This will bring to front a window containing the
symmetries operators, as defined by the
program suite. Swiss-PdbViewer uses the space group
definition fom the CRYST1 Line of the pdb file to try to
guess which space group the protein belongs to in order to
set the file directly at the proper location. All you need
to do to build the three symmetries is to click on the space
group header (which appears in red).
18 4 4 P21212 PG222 ORTHORHOMBIC
The original pdb file (not the one that is currently in
memory) is then used to contruct the symmetries and each
symmetry will appear in a new layer whose name indicates
which transformation was applied. Swiss-PdbViewer will try
to construct the symmetries as close as possible from the
current layer, in order to let you examine the
Now use the "Groups close to an other Layer" item of the
"select menu", choose the "Display only Groups that are
within" radio button, set 2 Å as a cutoff value, and
check the box "act on all layers". This lets you observe
which residues are involved in protein-protein contacts. In
this case, as the cutoff value is small, only residues
containing atoms too close to each other will be displayed.
As you can see, the water molecule that I have added is in
fact already present under the name HOH157.
Now we will populate the unit cell by doing some
Color by Layer, and make sure the Current layer is the
Use the "Translate Layer along unit cell" item of the
Tool menu. A window appreas, which contains the various
Click on the "0+0" line, and observe how the yellow layer
has been translated along the green axis of the unit cell
Now click on the "0-0" line while maintaining the
Control Key down. Observe how the yellow layer stay in
place, and a new layer appears, translated down the green
Now sitch the curent layer to "-X-Y-Z" (the blue layer).
And Click on the "+00" line while maintaining the Control
Key down. Again a new layer is created, this time with a
translation along the red axis (axis a).
Color by layer, and you should see someting like that: