In this example, we will learn how to apply
non-crystallographic symmetries and build a full tetramer
from a pdb file containing only a monomer of a
Step by Step
open file pdb file 1LDM (provided with the
tutorial package) and have a look
at it, rotate it. Did you ever wondered how it was possible
that the first six N-terminal amino-acids were out in the
solvent and not properly folded around the protein? Haven't
you learned that proteins were globular and tightly folded?.
Now, reset orientation (Edit menu), and open three more
copies of the pdb file. (You can use the 1LDM item at the
bottom of the File menu, as Swiss-PdbViewer remembers files
recently opened). Each copy is loaded into a new layer.
Now select all residues in all layers (hold down the
shift key while invoking the Select All item of the Select
Make the second layer active (use the control Panel popup
menu to switch among layers).
Click on the little text icon in the main display window.
This will let you consult the pdb file as a text file, which
is useful to have a look at the annotations.
Scroll down the pdb file until you find MTRIX lines (they
are just before the ATOM lines). You can see 9 lines MTRIX.
They represent three transformation matrices, and allow you
to build the non-crystallographic symmetries of the protein.
MTRIX1 1 -1.000000 0.000000 0.000000 0.00000
MTRIX2 1 0.000000 -1.000000 0.000000 0.00000
MTRIX3 1 0.000000 0.000000 1.000000 0.00000
MTRIX1 2 -1.000000 0.000000 0.000000 0.00000
MTRIX2 2 0.000000 1.000000 0.000000 0.00000
MTRIX3 2 0.000000 0.000000 -1.000000 0.00000
MTRIX1 3 1.000000 0.000000 0.000000 0.00000
MTRIX2 3 0.000000 -1.000000 0.000000 0.00000
MTRIX3 3 0.000000 0.000000 -1.000000 0.00000
Click on the first line of the first MTRIX record.
This will load the transformation matrix into a dialog.
Simply click on OK, and the transformation will be applied
on the current layer.
Now make the third layer active with the control panel
pop-up menu, and click on any line of the second
group of matrix, and apply the transformation.
Now make the fourth layer active with the control panel
pop-up menu, and click on any line of the third group
of matrix, and apply the transformation.
Now, color by layer (in the color menu), and observe your
full functionnal unit. As you can see, the first 6
N-terminal amino-acids are no longer isolated in the
We will now observe which residues are making
Make the first layer active (the yellow one).
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 a 5 angstroms as a cutoff value,
and check the box "act on all layers". Thnis lets you
observe which residues are involved in protein-protein
Now repeat the operation but without the ckeck on "act on
all layers". Every residue within 5A of any residue of the
current layer only will be selected. In this case,
only residues close to a "yellow" residue.
Change the active layer to the second protein (the blue
one) and do it again, to fully understand how this tool