MOLECULAR MODELING FOR BEGINNERS
Tutorial For Deep View (Swiss-PdbViewer)
Tutorial Revised for Version 3.7b2, 2000/12/22
Gale Rhodes
Department of Chemistry
University of Southern Maine
Portland, Maine, USA 04103
Author of
Crystallography Made Crystal Clear
A Guide for Users of Macromolecular Models
2nd Edition, Academic Press, February 2000.
Thanks to students in my 1997 through 2001 biochemistry courses, to Nicolas Guex, and to online users of this tutorial and for your many helpful suggestions. I invite and appreciate comments, corrections, and suggestions.
Overview
This tutorial provides an introduction to macromolecular modeling with Deep View, including review of many basic concepts in protein structure. You will first learn how to obtain structure files for viewing, and then carry out exercises in manipulating, analyzing, and comparing protein structures. Sections 1 through 6 give the essentials that everyone will need for using the program as a basic molecular viewer. Sections 7 through 11 add operations of intermediate complexity, such as working with multiple chains and models.
Deep View (formerly called Swiss-PdbViewer, but try saying that six times fast) is a friendly but powerful molecular graphics program. It is designed for use with computing tools available from the Expert Protein Analysis System, or ExPASy Molecular Biology Server in Geneva, Switzerland. While Deep View is simple to use for viewing structures and creating vivid illustrations for demonstration, publication etc., it also includes several analytical features:
-It can find hydrogen bonds within proteins and between proteins and ligands.
-It allows you to view several protein structures simultaneously and superimpose them to align their structures and sequences.
-It allows you to examine electron-density maps from crystallographic structure determination, to judge the quality of maps and models, and to identify many common problems in protein models.
-It computes electrostatic potentials and molecular surfaces, and carries out energy minimization.
-For proteins of known sequence but unknown structure, Deep View submits amino acid sequences to ExPASy to find homologous proteins, onto which you can subsequently align your sequence to build a preliminary three-dimensional model. Then Deep View submits your alignment to ExPASy, where the SWISS-MODEL server builds a final model, called a homology model, and returns it to you by e-mail.
The program is under continuing development by Nicolas Guex & Manuel C. Peitsch of Geneva Glaxo Welcome Experimental Research. Thanks to Glaxo, Nicolas, Manuel, and their colleagues for making this marvelous tool available to everyone.
Conventions Used In This Tutorial
In this tutorial, instructions for giving a command or using a menu appear in consistent formats. Usually, such commands appear at the beginning of a new line. Here are some sample instructions and their meanings:
<return>
means press the key labeled return on the computer keyboard. All key-press instructions are enclosed in brackets of the type >, while names of keys in written text are underlined.
Display: Backbone
means pull down the Display menu and select Backbone. All menu instructions are in bold type with a colon separating the names of menus, submenus, and commands.
heading: show
means click on the word show, which is the small heading of the show column in the Control Panel.
PDB File Names -- A Slight Departure from Convention
PDB file names consist of a number followed by three characters -- for example, 1HEW. Although it does not follow common convention, I (try to remember to) use capitals for the letters of PDB file codes, primarily because many file names contain the number 1 or the letter L, which are identical in most fonts if not capitalized. The number zero practically never occurs in PDB file names, so there is little chance of confusion with the capital letter O.
DIRECT IMPORT OF PDB FILES
Deep View 3.7 can obtain PDB and ExPDB files directly, without a browser. ExPDB differ from original PDB files It can also directly import other types of database information. To enable this feature, use Prefs: Network to make these settings:
· File Server IP Address: www.gwer.ch
· Port: 27000
Use File: Import to obtain files by PDB code.
Basic Tutorial For Deep View
1. Getting Started
NOTE: Plan to work at least through section 4 of this tutorial without stopping. Thereafter, the end of any section is a convenient stopping point. Beyond section 6, you can take sections in any order.
ADVICE: Take time to TRY OUT different features of the program. Especially at the end of each section, you can play around without losing the continuity of the tutorial. By this you will discover additional features, and you will develop a personal style of using the program that will make it a more powerful tool in your hands.
You will start learning about Deep View by looking at the enzyme lysozyme in complex with the trisaccharide inhibitor tri-(N-acetylglucosamine) or tri-NAG (see a biochemistry text if you want to know more about lysozyme). Atomic coordinates for this model are contained in the Protein Data Bank file with code 1HEW. If you have the full set of files for Deep View, you will find this file with the name 1HEW.pdb in the folder entitled hel. Otherwise you may import the file directly from the PDB and save it to disc in your personal folder.
Start the program either by double-clicking the SPDBV alias at the desktop, or by going to the start menu of you PC, choose program, and find SPDBV. When the program starts a menu bar will appear on you desktop. From the File menu choose Open PDB File:
File: Open PDB File ... (remember the tutorial conventions: this is a menu command)
Find and open the file 1HEW.pdb. Click OK on any dialogs that appear.
2. Windows and Help
If a window named inputlog.txt is open, close it. Before getting started, you will make a couple of settings that streamline initial program operation.
Prefs: General
On the General Preferences form, make the following settings:
· Uncheck "Show the 'setting depth to 256 colors'.. ."
· Uncheck "Show splash screen at startup."
· Uncheck "Show log file upon loading."
· Click OK.
Deep View has two main windows, the display or graphics window, which shows the three-dimensional structure (the PDB file) and the Control Panel.
The graphics window and the buttons on the Tool Bar above it are used to view and manipulate the model, measure distances and angles between atoms, calculate and display hydrogen bonds, superimpose structures, mutate residues and build new residues into an existing model, these and many other features usually needed for work with protein structures.
The Control Panel (usually appears on the right) may be open by the command Wind: Control Panel. It lists the amino-acid residues within a structure and the type of secondary structure to which they belong. You may use the Control Panel to select residues, switch between structures, if you have red few into the program, choose which of the structures various commands will affect. You may also label residues, color them in different colors, display Van der Waals surfaces, make schematic ribbon-type pictures, etc. You must click on any of the windows to make it active. The first click on an inactive window activates it, but does not cause other changes.
Another useful window available is the Sequences Alignment window (Wind: Sequences Alignment). This window will appear below the graphics window and shows the amino-acid sequence of the protein. It can be used when the sequences of proteins which were red into the program need to be compared. It can also be used for finding a particular residue within a structure (pointing the mouse onto that residue will cause it to flash).
Ramachndran Plot window
You can use the Ramachandran Plot to judge the quality of a model, by finding residues whose conformational angles lie outside allowed ranges. You can also display and change conformational angles in the model. Each dot (actually, a tiny cross or square) on the diagram will give the phi and psi angles of a residue in the protein. You first need to select the residues for which you want phi and psi angles to be displayed. To select all residues follow the command: Select: All
The color of the residues listed in the Control Panel changes from black to red (and in the Sequences Alignment window, from white to purple). The new color means that a residue is currently selected. Some Deep View commands affect only the selected residues.
To display the Ramachandran Plot: Wind: Ramachandran Plot
The window appears in the upper left. Have a careful look at this window. Are there any residues with phi, psi angles outside the allowed region ?
Import the file 6ADH from PDB, select all residues and display the Ramachandran Plot again. How do these two structures (lysozyme, which you already have and alcohol dehydrogenase) differ from each other ? This small exercise demonstrates how different the quality of protein structures may be. Something to keep in mind.
Close the 6ADH model by first choosing it from the Control Panel. You do it by clicking anywhere on the Control Panel window to make it active. Then click on the top of the panel where 1HEW is displayed. This will show a list of structures which were input into the program (called layers in the program), in this case 1HEW and 6ADH. Choose 6ADH from the list. Then close this layer by File: Close.
Wind: Layer Infos
The small Layer Infos table appears at the upper right. This table provides control of multiple protein models, allowing you to choose which models are visible, which models can move, and which models have certain features on display.
Each window displays a small red question mark. Click the question mark for help in using that particular window. For more information about commands and functions in the full User Guide for Deep View, look under the Help menu.
On the Tool Bar of the left, there are two symbols, a globe and a little dog-eared piece of paper. By clicking the paper you may see the PDB file of the protein currently on display.
For now, close the Align, Ramachandran Plot, and Layer Infos windows.
For more information about windows you may use the Deep View User Guide.
3. Manipulating the Model
Click on the graphics window to make it active. Click Zoom/Center button (the first button on the left). This button automatically zooms and centres the structure which is currently on display.
The movement of the model is controlled by three buttons. From left to right, starting from the second button on the Tool Bar, they translate, zoom, and rotate the model. Try each one: first click to activate the button, then drag the mouse left and right to see the effects. Notice that the cursor changes to show you which button is selected. Watch the cursor as you press the tab key repeatedly. Pressing tab cycles through the three movement functions from left to right. Now hold down the shift key while pressing tab repeatedly. This action cycles through the movement functions from right to left. If you keep your left hand at the keyboard while using the mouse, you can select any movement function in a single operation, without having to point and click on the buttons.
Spend some time manipulating the model to get used to the controls. Then press the right mouse button. This key centers the model and adjusts its size to fit the screen, without rotating. This is a very handy feature. Whenever the view becomes awkward, just press either of these keys to give a convenient view of the model. You will achieve the same result by clicking the Zoom/Center button on the Tool Bar.
Because Deep View displays only in wireframe, without depth cueing, stereo viewing will help you to get an impression of the structure in three dimensions.
Display: Stereo View
<help>
Deep View displays a stereo pair. Press help to adjust size and centering. You may need to adjust stereo settings further in order to achieve comfortable viewing.
Prefs: Stereo Display
Set stereo view rotation and separation. Try a rotation of -4 degrees (minus four) for cross-eyed viewing. Decrease the separation if the views are too far apart to fit the window. Each time you change the separation, close the dialog, zoom/center the model and see how well it fits the window. For any functions that require clicking on an atom while viewing in stereo, you must click on the atom in the left image. The right image does not respond to mouse clicks.
Here's another handy manipulation feature: right-mouse click the name of a residue in the Control Panel. Deep View selects the residue and centers the view on its alpha carbon (CA). Zoom in very close to the model, so that the centered residue fills the screen. This feature is very useful for jumping to a specific residue in your model.
Take time to explore the tools introduced in this section.
4. Selecting and Displaying
The Control Panel can be used to select, display, or hide parts of the model. In the Deep View User Guide, parts of the model are called groups, meaning amino-acid residues or hetero groups (anything bound to the protein like inhibitor, ligand, water – all are called hetero groups or hetero atoms) like the three NAG residues in the lysozyme inhibitor. Selecting groups does not change the display. But most actions that you take on the model affect only the currently selected groups. The Control Panel lists all the groups in the model, and gives you fast and powerful means to select, hide, and display.
Click anywhere on the Control Panel window to make it active. First, simply scroll down to the bottom of the list to see how many amino-acid residues the protein contains, and to see how the hetero groups are named at the bottom of the list (hetero groups are always listed last). The tri-NAG inhibitor is listed as three residues of NAG, numbered 201 to 203.
Now click and drag, starting on the word GLY4 at the top of the window, dragging down to GLY16 and releasing the mouse button. All group names from GLY4 through GLY16 should turn red. Groups printed in red are now selected. The simplest way to select a small number of residues is to click their names and drag to select a range of them.