Molecular Visualization using Swiss PDB Viewer

OUTLINE

Step 1: Searching the PDB to obtain PDB files

Step 2: Loading a PDB file into Deep View
Step 3: Working with Deep View Tools

The Control Panel

The Main Toolbar: Rotation, Zooming and Centering
Changing colors

Exercise 1

Step 4: More Viewing Tools: Slabs, Selecting Specific Residues and Ramachandran Plots

Step 1: Searching the Protein Data Bank to obtain PDB files

To start, we need a PDB file and the Swiss PDB-Viewer. Open a web browser of your choice and
follow the link below to the Protein Data Bank website. Also open the Swiss PDB Viewer program.

1. Go to the Protein Data Bank.

This is THE repository for protein structural information. Crystallographers and

other structural biologists enter the data they have collected on their protein
structure in this database. Each entry in the database is given a 4 character
alphanumberic identification number. This number is unique for each structure and
is used to file it in the database. Associated with each entry in the database is a
series of information relating to that protein.
2. Find the PDB entry for bovine beta-trypsin.

You may do this in two ways (try both):

1. In the search box enter bovine beta trypsin and press the search button.

You should find that there are many entries for this query. These include many structures of bovine beta-
trypsin, trypsin inhibitors and also structures with bovine beta-trypsin complexed with several
inhibitors. We want a particular structure so follow step 2.
2. In the search box enter 1TPP

You should find one entry on the results page. This is the entry that we will work with during this
exercise. You will need to download the .pdb file, get information about this structure from the .pdb file
and view the structure using the Swiss PDB Viewer.
4.

Step 2: Loading a PDB file into Deep View

1. Open the Swiss PDB-Viewer. If you do not have this program on your computer you can
download it from the SwissPDBViewer site. It is available for Mac and PC. The controls for
these programs look similar, but are not entirely identical. This tutorial was generated using the
Mac version that we have loaded into the computers in the CCMML.
2. Run the SwissPDB Viewer program (choose the appropriate folder in the Applications folder on
the Mac, select the appropriate folder on a PC). You should see a program bar appear that looks
like this:

3. In the file menu click on Open in the menu options at the top of the screen and choose the 1TPP
file you just downloaded.
4. The structure of 1TPP should appear as well as a text file (a log file) that will appear on top of
the program bar. Close this text window so that what you see is the program bar and the stick-
model of the protein structure in the window below the bar. You should now have something
that looks like this:
 5. To view the .pdb text file for this structure click on the little "page" icon in the top left of the

program bar.

This opens the .pdb text file in a new window. You can get a lot of information about your protein and
this structure from this file. You will need a lot of this information to complete the protein structure
assignment.

On the page with the pdb file listed, you can explore the raw data that will
be converted into your great-looking 3-D images in a couple minutes. This
may look confusing at first. Remember that this info is set down in a
particular format so that all structures can be displayed, archived and
understood in the same fashion. Some of the important line items and their
descriptions are listed below:

A listing Information given

of all the
atoms in
the
structure,
the amino
acid or
heteroatom
that they
belong to
and the
coordinate
s of those
atoms.
Location
of
disulfide
bonds
Residues
that are
included in
sheets
Residues
that are
included in
helices
Heteroato
ms are
listed here.
These are
atoms that
are not
part of the
primary
sequence
of the
protein.
These can
include
cofactors,
metals or
bound
inhibitors.
The
primary
sequence
of amino
acids in
the
structure
This
section
contains
additional
informatio
n about the
structure.
It includes
all the
informatio
n the
authors
feel is
necessary
to properly
cite,
describe or
explain the
structural
informatio
n. Where
this work
was
published
The
investigato
rs that
performed
the study
The
organism
the protein
comes
from The
protein
that is
described
Term

ATOM
SSBOND
SHEET
HELIX
HET
SEQRES
REMARK
JRNL
AUTHOR
SOURCE
COMPND
Gives a basic description of
the structure
HEADER

Step 3. Working with Deep View Tools: The Control Panel, Rotation Tools and
Changing Colors

Next we will work with this structure. Our initial goal will be the generation of a ribbon diagram and a
space-filled diagram that highlights some key structural features of trypsin. It is helpful to be familiar
with the basics of the mechanism of serine proteases. If you do not remember this from Chem 371 then
review this in your Lehninger text. In this text the mechanism of the serine proteases is examined using
chymotrypsin, the mechanism of trypsin is similar and also uses the classical catalytic triad (Ser, His,
Asp) however the specificity of trypsin is different, it cleaves following basic amino acid residues.
During our exercise we will examine the structure of the inhibitor that is bound within the active site
and understand why it is bound where it is bound and what aspects of the natural substrate it mimics.

NOTE: Depending on the speed of your computer and its graphics capabilities you may or may not
want to toggle on the 3D rendering options in your window. To turn these features on go to the Display
menu and turn on 'Render in Solid 3D' and 'Use OpenGL rendering.' You can play with these options to
see which (or both on better computers) works best with your system. If neither works well, turning
these features on only when you are finished working with the model (rotating, coloring etc.) or want to
briefly see your model will work.
Deep View operates in as a series of windows. This is useful because you can open and close the windows as
you need them. The main toolbar will always be open. It looks like this:

The other windows are opened from the Window menu ("Win") located at the top right. These will open as
independent windows and can be opened and closed at any time.

The Control Panel

1. Open the control panel

In the
main
toolbar,
click on
Window
("Win")
and then
Control
Panel.
The drop
down
menu is
shown to
the right.
2. The control panel, a long window will open to the right of the main window. The main features of
this window are displayed in the aqua box below. Exercises to test your working knowledge and help in
the completion of our initial tasks are indicated in the Exercise 1 yellow box below (be patient, there's a
lot to get used to before you can work with the structure!).

The Control Panel Explained

The Explanation
small
letters
to the
left of
the
group
name
indicat
e
wheth
er this
residu
e is
locate
d in a
helix
or a
strand.
These
are
differe
nt
from
the
capital
letters
that
can be
locate
d to
the left
of
these
letters
that
indicat
ea
separat
e
chain.
Drop
down
menu
for the
color
option.
You
use
this
drop
down
menu
to
choose
wheth
er you
are
changi
ng the
color
of the
backb
one,
backb
one+si
dechai
n,
sidech
ain or
the
ribbon.
'col'
stands
for
color.
Highli
ghting
particu
lar
residu
es and
clickin
g on
this
box
brings
up a
dialog
ue box
that
allows
you to
change
the
color
of the
selecte
d
residu
e.
"ribn"
stands
for
Ribbo
n. If
checke
da
ribbon
will be
traced
throug
h the
backb
one
and it
will be
drawn
as a
helix
or
strand
depen
ding
on the
classifi
cation
of that
amino
acid
(see
K)
This
symbo
l
stands
for
'dots
surfac
e' or
the
van
der
Waals
or
accessi
ble
surfac
e area
of the
protein
.
When
checke
d the
vdW
or
accessi
ble
surfac
e will
be
shown.
The
drop
down
arrow
allows
you to
select
which
surfac
e will
be
displa
yed.
"labl"
is
short
for
Label.
If this
is
checke
d the
amino
acid
will be
labele
d in
the
structu
re with
the
three
letter
abbrev
iation
and
the
residu
e
numbe
r.
These
labels
can be
change
d in
the
Prefer
ences
menu
"side"
is
short
for
side
chain.
If this
is
checke
d then
the
side
chain
for
that
particu
lar
atom
will be
shown.
"show
" is
short
for
show
backb
one. If
a "V"
is
listed
(a
check
in
Deep
View)
in this
colum
n then
the
backb
one for
that
particu
lar
atom
will be
shown
The
'group'
colum
n lists
the
amino
acid
(in
order
from n
to C
termin
us)
with
the
hetero
atoms
at the
bottom
of the
list. To
the left
of the
group
colum
can
also be
a
colum
n with
letters
from
A-Z. If
there
is
more
than
one
amino
acid
chain
in a
molec
ule,
this is
shown
by
these
letters.
If
checke
d, you
can
move
the
structu
re
around
Label

K
J
I
H
G
F
E
D
C
B
This check-box
toggles the
visibility of the
structure in this
layer
A

This checks/unchecks ('V') next to a residue

clicking within a row
and activates the feature in that column
This selects all groups that you click on
option+click on a group while control is pressed. This is useful for
selecting a group of residues and especially
(control+click on a PC) useful if they are not continuous within the
sequence.
shift+click within a This checks/unchecks all residues in that
column column within a layer
This checks/unchecks all residues in that
control+shift+click
column within all layers (if working with
within a column
multiple layers)
Control+Z Undo
The Main Toolbar, Rotation, Zooming and Centering

The main toolbar contains all the major tools for navigating the structure, moving the structure and
changing your perspective.

Label Description
A Clicking on this button centers the molecule on the screen
Clicking on this button changes your cursor to the 'hand' which allows you to move the
B
entire molecule or selection
 Clicking on this button changes your cursor to the zoom-in zoom-out cursor. Dragging your
C
mouse forward and back will zoom you into and out of the structure.
Clicking on this button changes your cursor to the rotate cursor. Moving your mouse side-to-
D
side and up and down will rotate the molecule or selection
Clicking on this changes the rotation from a global rotation or a rotation about the axis of
E symmetry of the molecule. Often this is useful to play with when you are trying to get a
particular angle and can't quite get the structure to move the way you would like.
F Toggles between moving the entire structure or just the selected residues.

Changing Colors

You can change the color of individual residues, ribbons, loops and strucures by selecting them
individually and in groups and then changing the color of the ribbon, sidechain, backbone etc. from the
Control Panel. You do this by selecting the down arrow under the 'col' option to change the item you
want to color and then use the small boxes next to the residue to change the color. There are other
options, however that give you important information and are easier to work with than selecting groups
within the control panel. These selections are found in the Color drop down menu in the Main Toolbar.
The box below describes the most useful features of this menu.

Label Information
Colors the
individual
atoms
A
according to a
standard color
scheme
Colors by the
type of amino
acid. Non-polar
B = grey, polar
=yellow, acidic
= red, basic
=blue.
Colors by
secondary
structural
element.
Helices are red,
sheets yellow
C and loops
white, by
default. You
may change
these colors in
the Preferences
menu.
D Colors by
 secondary
structure
succession
from N to C
terminus. This
colors by
wavelength of
the visible
spectrum from
N terminus =
violet to C
terminus =red.

Exercise 1: Using the above tools to view meaningful aspects of serine protease
structure.

Click on Outline, Control Panel, Main Toolbar and Changing Colors to return to the appropriate
sections above. Click on the icons above to return to this section.

Instruction Comments and Assignment Instructions (in bold)

Remember to turn off the side chains using the control menu. To make the ribbons solid, go
Prefs-->Ribbons and change the following options to make the ribbons solid:

1. Create a ribbon
diagram of trypsin.
Color it by
secondary structure
and then by
secondary structure
succession.

2. Place labels on
the N-terminal and Check "labl" next to these residues in the Control Panel
C-terminal residues
3. Make the
heteroatom(s)
Use checkmarks in the 'show' and 'side' columns for these heteroatoms.
appear in ball and
stick representation
4. Rotate the
structure so that Save a copy of this view by selecting Save-->Image in the File menu. Name this file
you best see the Initials01 (Example my first file was LML01). This can then be imported into the Protein
inhibitor bound Structure Exercise document. You will then write a descriptive caption for this picture
within the active that describes what is shown, highlighted and the overall purpose of the figure.
site and zoom the
structure in/out to Note: On a PC early versions of this program saved files as .tga files. These must be
best view the active opened in a photo editing program and saved as a different filename. On a Mac, this
site, while still doesn't happen. The files are saved as a .pict file. If you want to rename the file you can
retaining the entire open it in Preview or other photo editing software and rename it as a .tiff, .jpg or .gif for
protein in the import into a word processing program.
frame.
5. Now show the
structure of trypsin
in space-fill Use the control panel to change how the structure is shown.
showing the van
der Waals surface.
6. Color the
Remember to color both the backbone and side chain.
residues by Type
7. Retain the
inhibitor in ball-
and-stick form so
that it can be seen
within the active
site. Note the
possible
interactions Save a copy of this view by selecting Save-->Image in the File menu. You will write a
between that caption for this as described in the Protein Structure Exercise document.
inhibitor and the
protein that can be
seen through
analysis of the
information
provided in this
view.
Step 4: More Viewing Tools: Slabs, Selecting Specific Residue, Calculating H-bonds
and Generating Ramachandran Plots

The goal of this portion of the tutorial is to get you used to some more advanced features in Deep
View. This will allow you to select specific residues and allow you to display only those residues, or to
color these differently or display them in a particular representation. You can also compute H-bonds to
see which amino acids are connected non-covalently. If you combine these selection, image
manipulation and computational tools with the skills you learned above you will be able to create
images that convey a lot of structural information.
Ramachandran Plots

In addition to providing a tool for viewing structures, Deep View also allows you to examine the
phi/psi angles of the residues in the protein. In the Window menu is an option to generate a
Ramachandran plot for the protein you are viewing. This is a useful tool to find residues that may be
strained out of normal, allowed conformations, or to assess the quality of the protein structure (if 90%
of the residues have phi/psi angles outside the allowed regions, you may have some doubts!). To do
this you do the following:

1. In the control panel select all residues you want to see on the Ramachandran plot.

2. Choose Win-->Ramachandran Plot

A Ramachandran plot will be displayed. It will look like this:

Move the mouse over the symbols on the screen to show what residues are located in what area of the
plot. The residue numbe corresponding to those phi/psi angles will appear in the upper left corner of the
plot. This will allow you to investigate particular residues that fall within different areas of the plot.

Slab View

This option, located in the Display menu allows you to slice the protein and see successive cross
sections through the protein structure. When this option is checked, hold down the shift button on your
keyboard and move your mouse back and forth. This will 'slice' the protein into sections that you scroll
through with your mouse. In the preferences menu you can change the width of the 'slice' that you take
to allow finer and coarser views into the structure.

Computing H bond distances

Turning on this feature computes the H-bond distances between amino acids that are close enough to
form H-bonds and have functional groups that can make these interactions. There are two things you
must do to show these interactions:

1. You must compute the H-bonds. You do this by choosing Tools-->Compute H bonds

2. You must display the H-bonds by choosing Display-->Show H-bonds

To show only select H-bonds you can select particular residues in the Conrol Panel or using the
techniques shown below (blue table). After you do this then you:

1. Computer H-bonds by choosing Tools-->Compute H bonds

2. You display the H-bonds in a selection by choosing Display-->Show only H bonds from selection.

Selecting Specific Residues

There are several ways to select residues. In fact, there is a whole menu dedicated to the task of
selecting particular residues. That menu is described below.
This menu offers a variety of ways to
select residues. You can then decide to
color these a particular color, zoom in to
see these etc.

Some of the most useful:

None -- removes all selections. This is

useful to start fresh after making some
selections.
All -- Selects all residues
Inverse selection -- select some
residues, then choose this to choose all
residues but those currently selected.
Visible groups -- zoom in and then use
this to select those residues you have in
the current view.
Pick on screen -- choose then and then
click on particular residue(s). These will
be selected in the control panel.
Group Kind -- allows you to select a
particular amino acid, nucleic acid,
heteroatom, solvent molecule or
disulfide bond.
GroupProperty -- allows you to select
acidic, basic, polar and non-polar amino
acids.
Secondary Structure -- allows you to
select all residues in a beta sheet, alph
helix or coils. It also has options to select
all non-trans amino acids, amino acids
with phi/psi angles outside of core
regions or amino acids with phi/psi
angles outside of allowed regions.

Several of these options are also located

in the main toolbar. This will be
described below.
This icon, located in the main toolbar
allows you to select amino acids within a
defined radius . You click the icon, click
on a residue on the screen and the
'Display Radius' dialog box (shown to
the left) appears.
This icon doesn't do much in the way of
selecting in the Control Panel, but if you
click this button and then choose an
atom in the structure the view will
change such that the chosen atom is
centered in your view.