Move & Rotate
31 March 98
The Display Window
Molecules appear in wireframe representation in a black
window. Unlinked atoms appear as a small cross.
The default atoms colors are the following (this can be
changed in the preferences).
C --> white O --> red N --> blue
S --> yellow P --> orange H --> cyan
other --> gray
Besides, you can individually change the color of any
group using the Control Panel or
the Color Menu.
There is currently no direct printing feature. However,
you can export the content of the display window as a 72 dpi
bitmap picture that can be printed from your favorite
There is no way to increase the resolution of the image
directly within Swiss-PdbViewer. The workaround is to
increase the display window size (by clicking on the
leftmost tool) and then to increase the bitmap resolution in
your favorite graphic program before printing.
The Display Menu
Some features are regrouped under this menu. A quick
overview is given here.
- Show Control Panel
brings the control Panel to
- Show Layer Infos
brings the Layer Infos Window to front. From this window,
you can easily alter the displayed features of a layer
(Hydrogen, H-bonds, H2O,...). In addition, you can
control which layers will be allowed to "blink". Blinking
is a convenient way to compare proteins by displaying
only one layer at the same time and quickly switching
among the layers. For more details, click on the little
quiestion mark present at the top of the window.
- Show EDM Window
brings the Electron Density Map Window to front. This
lists the currently loaded electron density maps, and let
you alter what is displayed (unit-cell, coarse
contouring, sigma contouring value, color, dottet or
plain lines). Co ntrol-click on the name brings a more
complete dialog. For more details, click on the little
quiestion mark present at the top of the window.
- Show Ramachandran
brings the Ramachandran plot of
the currently selected amino-acids
- Show Sequences Alignment
shows the Alignment window, that is an alternate way of
selecting groups, and is useful to compare multiple
proteins that have been matched in 3D. Refer to the
tutorial section for more
- Show Text Window
brings the Text Window to front. The text window can
contain a PDB file, an on-line help, or any other text
file you might have open with the Open Text File item of
the file menu.
- Label Kind
This "pop-up" menu selects the kind of label to draw on
each group. By default it is the group name that appears
on the carbon alpha, but you can choose to display atom
names or atom type (see
Note: Labels are drawn only if a mark appear in front of
a group in the "label" column of the
Control Panel. Their
apparence can be changed in the preferences.
Note: This menu also permit to clear all the distances
informations that are added on the molecule each time you
measure a distance or an angle.
When this item is enabled, two Z clipping planes are
enabled. It allows you to go "inside a protein" without
having to see all periferical atoms. By default the
visible section depth (i.e. distances between the
two clipping planes) is of 10Å, but you can change
it in the "Display Window Settings" dialog. Initially,
the section is centered on z=0, but you can move the
clipping planes by holding the "shift key" and clicking
while you move the mouse, regardless of the currently
Note: The slab mode will display/undisplay an amino acid
entirely as soon as its CA (C1_ for nucleotides) is
in/out of the section defined by the two Z-clipping
planes. This prevent unlinked atoms and bounds to fly
around the display. However, this rule does not apply for
HETATM groups that can be so large that they actually
need to be clipped.
- Front View, Left View,...
The next group of articles allows to quickly "rock around
- Show Backbone Oxygen
For very large molecules, it is sometimes useful to see
only the backbone trace. (This menu can also be accessed
from the Layer Infos Window).
- Show Sidechains even when Backbone is
When checked, this menu allows the display of sidechains
even when no mark is present in the show column of the
control Panel. This can be useful for certain kinds of
final renderings with ribbon representation of the
protein. (This menu can also be accessed from the Layer
- Show Dots surface
When checked, this menu allows the display of van der
Waals surfaces. It supersedes the setting found in the
"dot" column of the Control Panel. Why? Because Dots
surface can be long to compute, and you may want to
temporarily undisplay them without loosing your
- Show Axis
When checked, the axis orientation of the first protein
loaded will appear at the top left of the screen. Note
that it is different from the axis that can be displayed
from the Layer Infos Window, that always appear at the
(0,0,0) coordinate of each concerned layer.
- Show Hydrogens
Toggle the Hydrogens display status. It is sometimes
easier to see something if H are temporarily undisplayed,
isn't-it ? (This menu can also be accessed from the Layer
- Show H-bonds
Same for H-bonds, providing that they have been computed
! (to compute H-bonds of the current layer, choose
the appropriate item of the "Edit" menu).
- Show H-bonds distances
Draw the distance between donor and acceptor at the
middle of each H-bond. When several H-bonds are very
close, some screen garbage can occur, and you may need to
rotate a little the molecule to be able to read the
distance. (This menu can also be accessed from the Layer
- Show only H-bonds from selection
Show only H-bonds whose one extremity belongs to the
selected groups (groups appearing in red in the control
- Show only groups with visible H-bonds
Allows to focus on important things. Very useful in
conjunction with the previous function:
Imagine that you want to display only groups that make
H-bonds with an enzymatic cofactor (NAD, ATP...) click on
NAD in the control panel (it is now the only selected
group), ask to "show only H-bonds from selection", and
then ask to "show only groups with visible H-bonds",
which will clean-up the view. Quite easy isn't-it ?
- Render with Q3D
This will generate a solid image with Apple
3D (which is available both on Mac and PC).
Colours, lights, appearance
and kind of renderer can be altered in the two
appropriate prefrences dialogs. During rela time
operations, the classic wireframe will be used in order
to have a better interactive feeling.