Basic Tutorial for Swiss-PdbViewer 3.0
Swiss-PdbViewer (SPdbV) is an easy-to-use and powerful molecular
modeling program. In addition to its many built in features, it is tightly linked to
an automated homology modeling server run by the Geneva Biomedical Research Center. For
proteins of known sequence but unknown structure, SPdbV submits amino acid sequences to
ExPASy to find homologous proteins, onto which a preliminary three-dimensional model may
be built. Then SPdbV submits the alignment to ExPASy, where a final model is built and
returned by e-mail.
Start the program
(Unless otherwise stated, "click" means a left mouse button
Double-click on the Swiss-PdbViewer icon to start the program. Click
anywhere on the startup banner to begin working.
Go to File > Open PDB file to locate and open
a pdb file, such as 1cca.pdb. Click on
OK; button on any dialog that appears. (You may accept default or change
Rendering Attributes settings).
Each window has a small red "?" (question mark). Clicking the question
mark will bring up help information about using that particular window. An alternative way
is to consult the Swiss-PdbViewer "Help" menu, which has help items for each
window. For detailed modeling instruction, do Help > Local Manual and your web browser will automatically load the User Guide
The SwissPdbViewer Windows
After the protein pdb file is loaded, SPdbV opens two windows: the Control Panel, and
the display or graphics window. The Control Panel is used to select, label, and color
residues. The graphics window and the tool buttons on it are used to view, manipulate, and
measure the model. Only the active window with blue caption color responds to mouse or
keyboard actions. The first click on an inactive window activates it, but does not cause
any other change. Three other useful windows may be made visible from the
Displayà Show Sequences Alignment
The narrow "Align" window appears below the graphics window, showing the
amino-acid sequence of the protein in one-letter abbreviations
Display > Show Ramachandran Plot
This window could be used to judge the quality of a model, by detecting residues whose
conformational angles lie outside allowed ranges. The Ramachandran Plot window may also be
used to alter the backbone: directly modify the f /y angles of a residue by dragging the little cross to its new
location. The rotation around either of the f or y axis during this operation may be constrained by holding down the
"9" or "0" key while moving the cross. By default it is the C-terminal
part of the protein that will move, as a little 'C' appeared just below the help icon (?).
To move the N-terminal instead, click on the 'C' for its changing into a 'N'. To move only
a part of the backbone (not the whole backbone up to the C-terminal), first break the
backbone after the last amino-acid that will move. This is done with the appropriate item
of the tool menu
Displayà Show Layer Infos
This table provides control of multiple protein models, Use it to choose which models
are visible, which can move, and determine certain display features for each model.
two small icons
Below the first tool button (Window Attributes), there are two symbols,
a globe (or protein) icon and paper icon. Click the paper icon to see the PDB file. Click
the globe icon to switch to little protein icon. The globe icon indicates that the
rotation takes place in absolute coordinates, while the protein icon indicates the
rotation is around their centroid. Hence the first option allows you to rotate the
molecule around any atom, providing that this atom has previously been centered
(translated to the (0,0,0) coordinate).
- Click on the graphics window to make it active.
- Click the first tool button in the left to bring up the "Rendering attributes"
dialog. These parameters could be adjusted for viewing convenience. (I.e. Adjusting
"Slab depth" is very useful while investigating active site or when an electron
density map is visible.
- The "Translate", "Zoom" and "Rotate" tool buttons are used
to manipulate the protein model. Click to activate the button first, then drag the mouse
around to see the effects (the mouse cursor appearance changes to match the active tool).
- Pressing "Insert" key or right clicking anywhere on the
graphics window moves and scales the visible molecules to fit the view.
Select and Display the model
- Press "Enter" - Display only selected groups and hide others.
- Press "+" on the numeric keypad - Add the selected groups to the view without
hiding non-selected groups.
- Right click column header - Check only the selected residues.
- Right click on residue Center the view on the residue, do not select it.
- All - Select all residues of the current layer. Holding the "Shift" key to
select all residues of all layers.
- None - Deselect all residues of the current layer. Holding the "Shift" key
to deselect all residues of all layers.
- Inverse Selection - Simply inverses the selection. For example: for selecting all
residues but basic ones, first select basic residues, then inverse the selection.
- Extend to other layers - This is typically used after a structural alignment has
been done. It allows selecting some residues in one layer, and automatically selecting
their counterparts in other layers. It is kind of useful to compare active sites of
- Pick on screen Select multiple residues directly form the screen.
"Esc" ends the selection. To add the picked residues to the previous selection,
hold the "Control" key down while invoking this command. Note: This command will
only allow selecting residues of the current layer. This is especially useful when two
residues of separate layers are exactly superposed, because only the residue of the
current layer will be selected.
- Group Kind - This submenu allows selecting residues by type (different type of amino
acid, nucleotide, HETATM, solvent and S-S bonds).
- Select Acidic amino acids - Select Asp and Glu.
- Select Basic amino acids - Select Arg, Lys and His.
- Select Polar amino acids - Select Asn, Gln, Ser, Thr and Tyr
- Select non Polar amino acids - This will select Ala, Cys, Gly, Ile, Leu, Met, Phe,
Pro, Trp and Val
- Helices, Strands, Coils - Select all the residues in the corresponding secondary
- Visible Groups - Select the residues currently visible. In slab mode, only select
groups within the view window.
- Reconstructed amino acids - Select residues whose sidechain has been reconstructed.
It should be noted that incomplete pdb files are completed upon loading.
- Neighbors of selected aa - Extend a selection around a previous selection.
- Groups Close to another chain - This is useful for investigating the residues at the
interface of two chains. (I.e. examining how dimers or multimers are bound to each other.)
- Groups Close to an other layer Similar as above.
- Accessible aa - Select residues in a certain surface accessibility.
- Groups with same color as - This allows picking a residue on screen, and selecting
all residues that have the same color. This is useful for changing groups
color from one kind (I.e. red) to another (I.e. yellow).
- aa identical to ref. - After a structural alignment has been done, invoke this
command to select residues that are strictly conserved between the current layer and the
reference protein (the first loaded).
- aa similar to ref. Similar as above, will select conserved residues. The
PAM200 matrix will be used, and the minimum score needed to be considered similar can be
modified in the "Alignment" Preferences. Decreasing this stringency value will
increase the number of amino acids considered as similar.
- non Trans aa - This will select residues whose w angle is
below a certain value. Typically residues are trans (around 178 deg.) This lets you select
distorted residues or look at cis residues.
- aa with phi/psi out of core regions - This will select residues that lay outside of
the "core" region (the region where most of the residue should lay).
- aa with phi/psi out of allowed regions Similar to preceding. Few residues
(except Gly which lacks a sidechain) should lay outside of the allowed regions.
- Show Control Panel - Bring the control Panel to the front.
- Show Layer Infos - Bring the Layer Infos Window to the front. This window controls
the display features of each layer (visible, movable, CA, H2O etc
- Show EDM Window - Bring the Electron Density Map Window to the front. This lists the
currently loaded electron density map, and controls how it is displayed (unit-cell, coarse
contouring, sigma contouring value, color, dotted or plain lines). Holding the
"Control" key brings up a more complete dialog.
- Show Ramachandran - Show the Ramachandran plot of the currently selected amino
- Show Sequences Alignment - Show the Alignment window, which is useful when comparing
multiple proteins that have been matched in 3D. It may aloso be used to select residues.
- Show Text Window - Bring the Text Window to the front. The text window could contain
a PDB file, an on-line help, or any other text files which have been opened with
File > Open Text File.
- Label Kind - This is used to select label display type. The default label is the
group name that appears on the a carbon, but other options
(atom names or atom type) are available.
- Slab - When enabled, only residues between the two Z clipping planes are displayed.
The default slab depth is 10 Å, but it may be changed in the "Rendering
Attributes" dialog. Initially, the slab is centered on z=0, but could be moved by
holding the "Shift" key and moving the mouse with the left key pressed. Note:
The slab mode will display/undisplay an amino acid entirely as soon as its CA (C1_ for
nucleotides) is in/out of the slab. This removes unlinked atoms and bonds from the
display. However, this rule does not apply for HETATM groups.
- View from View the molecules from different angles.
- Show CA trace only Display the "backbone" structure. (lines
- Show Backbone Oxygen Show or hide backbone oxygens.
- Show Sidechains even when Backbone is hidden - When enabled, this menu allows the
display of sidechains even when no check 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.
- Show Dots surface - When checked, this menu allows the display of van der Wals
surfaces. It supersedes the setting found in the "dot" column of the Control
Panel. Because Dot surface can take a long time to compute, it is often helpful to
temporarily undisplay them, modify the display, and then redisplay them without having to
change the set of dotted residues.
- Show Axis - When checked, the axis orientation of the first protein loaded will
appear at the top left of the screen. It should be noted that it is different from the
axis that can be displayed from the Layer Infos Window, which always appear at the (0,0,0)
coordinate of each concerned layer.
- Show H-bonds This command is available after H-bonds have been computed.
- Show H-bonds distances - Draw the distance between donor and acceptor at the middle
of each H-bond.
- Show only H-bonds from selection - Show H-bonds whose one pair belongs to the
selected groups (groups appearing in red in the control panel).
- Show only groups with visible H-bonds - Allows focusing on important things. For
example: In order to display only groups that make H-bonds with an enzymatic cofactor
(NAD, ATP...), click on the cofactor name in the control panel (it is now the only
selected group), then select "show only H-bonds from selection", and then
"show only groups with visible H-bonds", which will clean-up the view.
- Render with Q3D - This will generate a solid image with Apple
Quickdraw 3D. Colors, lights, appearance and kind of renderer can be altered in the
two appropriate preferences dialogs (Q3D rendering and Q3D light).
Swiss-PdbViewer "Preferences" menu
A default preferences file is created or altered each time the program exits. This file
contains the exact configuration present at the time the program exits. Several different
preference files may be used as "style sheets" for different modeling tasks.
Under Swiss-PdbViewer "Preferences" menu:
- Modify last Prefs dialog - Display the last preference dialog that could be
- Open - Replace the current settings (Default.prf) with those stored in the alternate
- Save - Saves the current settings in a file for future usage. Note that the current
settings are always automatically saved in the "Default.prf" file when the user
quits the program.
- General - This dialog mainly allows the user to alter the behavior of the program at
startup and when a file is loaded.
- Loading Protein Alter the protein loading attributes. For example, the
protein could be loaded with: color by secondary structure; a solid ribbon displayed
instead of the wireframe representation; superposition onto previously loaded proteins;
and a structural alignment computed.
- Real Time Display - In order to insure a "smooth" handling of real-time
molecule displacements, a number of options aimed to reduce the CPU load while the
molecule is moving are provided. If the number of lines needed to draw the display exceeds
the maximum, the program will first attempt to draw the molecule without stereo view, then
without hydrogens, and finally without sidechains. For extraordinarily large displays, the
program can be configured to draw only one group out of n.
- EDM - This dialog controls the display of electron density maps. The same map can be
simultaneously contoured at two different sigma levels with different colors. For fast
rendering, a coarse contouring along one or several of the unit cell axes may be used. The
unit cell axis are colored in red for a, green for b and blue for c.
Loading protein molecule: Select the
"Open" item from the "File" menu, or select one of the recently opened
proteins that appear at the bottom of the file menu, then the molecule will appear in the
Adding molecules: Same as loading protein
Exporting molecules: Molecule may be saved in the
exact orientation it appears on screen by choosing the "Save PDB" item of the
"File" menu. All atoms of the current molecule (the current molecule is the one
whose groups are listed in the control panel, and whose name appears in the Display Window
title bar) are exported, even if they are not displayed. The screen image may be saved as
a BMP file by choosing "Export Image". For a larger image, simply enlarge the
Display Window Size before exporting the image.
Merging molecules: Fragments coming from different
molecules may be merged to build a new entity. This is done by selecting in each layer the
groups that will appear in a new layer, and then use the "Create Merged Layer"
item of the Edit Menu. The "merged" molecule will appear in a new layer, which
can be renamed using the "Rename Current Layer" item of the "Edit
Discarding molecules: Remove all molecules by choosing the
"Close" item of the "File" menu. Remove the current molecule (the one
whose groups are listed in the control panel) by hitting the "Delete" key.