Basic Tutorial for Swiss-PdbViewer 3.0

Manual

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Overview

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Start the program

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Obtaining helps

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The SwissPdbViewer Windows

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Manipulate the model

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Select and Display the model

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Use Swiss-PdbViewer "Preferences" menu

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SwissPdbViewer File operation

 


Overview

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 Swiss-Model (http://www.expasy.ch/swissmod/SWISS-MODEL.html), 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 click.)

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).

 

Obtaining helps

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 "Display" menu.

Ball-bl.gif (925 bytes)Display Show Sequences Alignment

The narrow "Align" window appears below the graphics window, showing the amino-acid sequence of the protein in one-letter abbreviations

 

Ball-bl.gif (925 bytes) 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

 

 Ball-bl.gif (925 bytes)Display 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.

 

 Ball-bl.gif (925 bytes)Another 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). 

 

 Manipulate the model

  1. Click on the graphics window to make it active.
  2. 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.
  3. 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).
  4. 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

Ball-bl.gif (925 bytes)Under Control Panel:

Ball-bl.gif (925 bytes)Under Select menu:

 

Ball-bl.gif (925 bytes)Under Display menu:

 

Use 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:

 

SwissPdbViewer File operation

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 display window.

Adding molecules: Same as loading protein molecule.

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 Menu".

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.