To Develop Multiple Renderings: This description should be read alongside that for the next item discussing atom selection. The two concepts work hand in hand. First activate the Graphics form. All renderings for your molecule will be summarized in the blue browser list found on that form. To add a new rendering, click on the "Create New" button on the bottom of this graphics menu. Notice that an extra line appears in the browser listing. In the text entry blank under the words "Selected Atoms", type in an expression which describes the atoms that you would like to represent in a different style. For example, type segname RET in the entry blank. Then using the drop down menu next to the words "Drawing Method", choose a new representation for your selection. For example, choose "Licorice." You will notice that all retinal atoms in the bR protein change in the GL Display. However the rest of the protein will appear unaltered, since you have not replaced the original rendering style, you have just added a new definition to it.
Using Atom Selection: VMD has a powerful atom selection syntax from which you can describe groups of atoms in a variety of ways. Your first exposure to this syntax will probably come through the text entry box on the graphics menu. For beginners, remembering the details of this syntax can often be a chore, so we recommend that you click on the "Atom Name Lists" button in the graphics menu to help you out. If you do so you will be greeted with two browser windows listing properties from which you can identify groups of atoms. The items in the "Keyword" browser are part of the selection syntax. If you click on one of these keywords, you will notice that available options for that keyword show up in the browser at the right. For example, click on the keyword "segname." You will see that you can choose from the seven alpha helices, the retinal, water, and other bR atoms. For a beginner, the best way to use these browser windows is as follows: First hit the "Clear Changes" button at the bottom of the form. Then double-click on the keyword you will use. You will notice that this keyword appears in the text entry blank. Next, single-click each "Value" you would like to include as an option to this keyword. If you hit the "Apply Changes" button at the bottom of the graphics menu, your request will be updated. As a concrete example, hit "Clear Changes," double-click "segname", and single-click HEL1 and HEL2. You should see segname HEL1 HEL2 in the text entry box. If you do, hit Apply Changes and you will notice that only the first two alpha helices of the bacteriorhodopsin remain visible in the representation you are working with. Remember to hit the "Image Controls" button to get back to controls for drawing and coloring methods.
To Change Colors: First activate the color menu. You will notice two browser windows in the upper left corner of this form. These two windows (labeled "Category" and "Names") are your way of specifying items that should have their color changed. For instance, suppose your present coloring method is by segname (i.e. in the graphics form, the drop down menu next to the words "Coloring Method" is set to "SegName.") Also suppose that you really hate the present color of the sixth alpha helix. In the color menu you can change this awful color by clicking on the "Segname" entry in Category and the "HEL6" entry in the Names browser. A list of available colors will pop up in a third browser window on the form. Select your favorite color and VMD will update the status of the sixth helix automatically.
How do I Switch Between Orthographic and Perspective Viewing: With the rightmost mouse button, click and hold in the GL Display window to reveal the popup menu. Drag down to "Display Modes" and choose the appropriate setting.
How do I Display Objects as Wireframes: This can be done by means of the display menu. Open it and click on the drop down menu to the right of the word "Detail." Several options will appear, one of which is wireframe. Try experimenting with other options in the display form to familiarize yourself with available VMD features.
How do I Make an Object Transparent: On the graphics form there is a button marked "Transparent." Clicking it will make the "current" representation transparent.
How do I Pick an Atom: If you simply click on an atom in the GL Display, you will notice that a label for that atom pops up on the screen. Many times these labels are useful, but too many of them tend to clutter the view. To delete them, use the popup menu. Hold down the rightmost mouse button in the GL Display window and drag down to "Labels" for options on deleting labels.
How do I Save: Hold down on the rightmost mouse button in the GL Display window. Drag down to the "Save Config" option. Type a file name in the box which appears and click Ready.