This file contains transcripts of the video sequences
from Introduction to ISIS/Draw and WebLab ViewerLite.
[Introduction to ISIS/Draw]
ISIS/Draw is a flexible and useful chemical drawing package. It can be used to draw organic and inorganic molecules and ions.
First let's have a look at the ISIS/Draw window. Most of it is taken up by the white area, where the molecules are drawn. Along the top there is a normal windows menu bar and underneath that is a row of buttons called the toolbar. The buttons here are mainly to do with drawing cyclic structures.
Down the side of the window is another toolbar. These are the buttons you will use most often when drawing molecules in ISIS/Draw.
If the mouse is placed over any button and left there for a short while, a label will popup giving the button's name. Pay particular attention to the buttons on the left-hand toolbar, as these are the ones you will use the most.
The first thing we need to do is draw a structure; let's draw a molecule of butanoic acid.
Butanoic acid has four carbon atoms in a straight chain, so let's start by adding these. To draw a chain of carbon atoms, we click on the single bond tool. Now we place the mouse pointer in the white area. Notice how the mouse pointer changes when a particular tool is selected.
To draw a carbon-carbon bond, we hold down the left mouse button and drag. A line appears, signifying a carbon-carbon single bond. Release the mouse button to complete the bond. To add another carbon to the chain, click on the carbon at the end of the chain and drag to form another bond.
Now we need to draw the carboxylic acid group. First let's draw the double bond to oxygen. Using the bond tool, draw a bond vertically upwards from the end carbon. To change a single bond to a double bond, we click in the centre of an existing single bond. From the vertical toolbar we select the atom tool. Click on the free end of the double bond and a drop-down list appears. Scroll down and choose the letter 'O'; this puts the oxygen atom in. Now for the OH group. Using the bond tool, draw another single bond out from the end carbon. Using the Atom tool, select the letter 'O' from the drop-down list.
We can tell ISIS/Draw to show hydrogens. Under the Options menu we select 'Settings' and on the 'Chemical Drawing' tab, pull down the 'Show hydrogen labels' list. There are various options. 'Hetero' means heteroatoms like oxygen and nitrogen. 'Terminal' means carbon atoms at the ends of chains. We'll select 'On Hetero or Terminal' for butanoic acid. You can also change several other settings, like bond lengths and fonts in the Settings box. Clicking 'OK' alters the settings for the current sketch. Clicking 'Save' will alter the settings for all future ISIS/Draw sketches.
Some of the buttons on the left-hand toolbar have little arrows in the bottom right-hand corner. This indicates that the button has alternative features. Holding the left mouse button down over one of these buttons will reveal the extra features. For example, the bond tool we just used to draw butanoic acid has extra features. The button can be used to draw double and triple bonds. Another example is the wedge tool, which can be used to specify stereochemistry or create flying-wedge diagrams.
ISIS/Draw saves files in sketch format. These can be read by WebLab, or alternatively, structures can be copied from ISIS/Draw and pasted directly into WebLab. To select a molecule, click on the 'Lasso select' button at the top of the vertical toolbar. This button also has alternative features. Using the select tool, draw around the butanoic acid molecule. Black squares appear around the structure to indicate that the molecule has been selected. Then from the Edit menu, select 'Copy'. This copies the butanoic acid molecule to the Windows clipboard and it can then be pasted into another application.
ISIS/Draw has a range of other functions that you may need to use at various points throughout this course. Details on how to carry out specific tasks will be given in the multimedia programs as you work through them. You can find more about them in ISIS/Draw by pulling down the menu labelled Help.
From the Help menu, we select 'ISIS/Draw Quick Start'. This is a 14-page help file which is designed to be printed. You will find it useful to print this document and have it as a handy reference as you work through the course.
This completes our introduction to ISIS/Draw.
[Introduction to WebLab]
WebLab ViewerLite enables you to get a three dimensional view of molecules. More importantly, you can manipulate the molecule and move it around so that you can view it from a range of different angles to get a real feel of the shape of the molecule.
First let's have a look at the WebLab window. Most of it is taken up by the black area, where the molecules are displayed. Along the top there is a normal windows menu bar and underneath that is a row of buttons called the toolbar. The buttons here are just handy shortcuts to the most commonly used menu items.
Down the side of the window is the tool palette. These buttons allow you to change the view of the molecule and its shape.
At the bottom of the window is the status bar that will show information about the molecule you are looking at.
If the mouse is placed over any button and left there for a short while, a label will popup giving the button's name, and a longer description appears in the status bar. Pay particular attention to the five buttons on the left-hand side in the tool palette, as these are the ones you will use most.
The first thing we need to do is to import a structure; to do this we click on the 'open' button on the toolbar. It's the second one from the left, and looks like a folder opening.
We are now presented with a list of different files that correspond to different structures. Let's open the file called butanoic acid. Clicking 'Open' loads the file into WebLab.
A molecular representation of butanoic acid appears in the Weblab window. This is a ball-and-stick representation. The 'Display Style' button on the toolbar allows us to change this representation.
A dialog box appears that has several sections to it, but for now concentrate on the choice of representations on the left. Clicking on the one labelled 'CPK' followed by clicking 'OK' changes the ball-and-stick structure to a space filled model.
WebLab offers several different display styles. For example, selecting 'line' and then click OK changes the display to a wireframe model of butanoic acid.
We will now return the display style to ball-and-stick and again click 'OK'. This gets us back to the ball-and-stick model of butanoic acid. The 'scaled ball-and-stick' option draws the spheres with their atomic radii. Bear in mind these radii are often different in molecules.
Now we'll look at how to move the structure using the tools on the tool palette.
The structure can be moved around in the window using the translate tool. This is the one with four arrows pointing straight out from it. You can use the popup labels to identify the button if you need to.
When the cursor is positioned in the centre of the WebLab window, the cursor changes to let you know which function you are about to perform. Holding down the left-hand mouse button, and moving the cursor to the right or left, or up and down, moves the molecule accordingly. Notice that while it is moving the structure changes to a wire framework model to speed up the drawing.
If you happen to move the molecule right off the screen you can always click on the 'Fit to Screen' button on the toolbar, as demonstrated here. This will re-centre the molecule.
The structure can be enlarged and reduced by clicking on the zoom button on the tool palette. This is the one that has a large arrow on the top and a smaller one on the bottom.
The cursor is positioned in the centre of the WebLab window, and the left-hand mouse button held down. Moving the cursor up or down changes the size of the molecule.
If your mouse has a wheel between the buttons, you can zoom in on the molecule at any time by rolling the wheel backwards and forwards, as demonstrated here.
The structure can be rotated by clicking the the 'Rotate' button on the tool palette.
Again, the cursor is placed in the WebLab window and the left-hand mouse button is held down. Moving the cursor left or right rotates the structure about the vertical axis and moving it up or down rotates it about the horizontal axis. Holding the shift button down, whilst moving the mouse with the left button depressed, rotates the structure about an axis coming out of the screen.
Now let's return the structure to its linear form, from left to right across the window.
So far we have left the structure intact while we have manipulated it. However, we can carry out rotations about single bonds using Weblab. This is done using the Torsion tool, that has the curly arrow on it.
The cursor is positioned exactly on any carbon-carbon bond of the butanoic acid molecule. Clicking on the centre of this bond and holding the button down, whilst moving the mouse pointer, leads to rotation about the bond. The angle of rotation, and its size, is shown in green. This is one of the more difficult manipulations to perform. If you find nothing happens when you click the mouse, you have not clicked on the centre of the carbon-carbon bond. It is a bit tricky to get exactly the right place, and you might find that changing the representation to line, rather than ball-and-stick, makes it easier find the right spot to click.
WebLab has a range of other functions that you will need to use at various points throughout this course. Details on how to carry out specific tasks will be given in the multimedia programs as you work through them. You can find more about them in WebLab by pulling down the menu labelled Help.
From the Help menu, we select 'Help Topics', and click on the 'Contents' tab. In this section, the various program options, menus and techniques are explained. In the 'Toolbars' section, you will find help on the operations we have performed in this sequence. The 'Index' and 'Find' tabs allow you to search by keyword.
This completes our introduction to WebLab ViewerLite.
