We have replaced most of VMD lite’s functionality by Molecular Modules, a web-based molecular visualization resource.
Although VMD is useful for the trained scientist, its extensive toolset naturally takes time to understand and effectively use. We have developed VMD lite, a graphical user interface, as a plugin that provides many of VMD’s powerful capabilities in a simplified format. Alongside the GUI we have written self-guided lesson plans that integrate with the typical high school curriculum. These lesson modules are designed in accordance with the Next Generation Science Standards, leading the student to critically evaluate relationships between important concepts in molecular biology, physics, and chemistry. This software is supplied free through VMD, and its database of self contained lesson plans will be continually modified and extended to reflect current curricula.
Using VMD lite
To use VMD lite, first download the latest version of VMD. Load VMD. you will see a display similar to what is shown below.
On the VMD Main window, select the drop down menu “Extensions” and choose “Tk Console”.
A new window, the Tk Console, will appear.
In the Tk Console, type “package require vmdlite” and hit enter.
Then type “vmdlite” and hit enter.
You will see the main VMD lite page open. From here you have the option to load the lesson modules or open Sandbox mode.
In sandbox, you may load a molecule from the list provided. Once loaded, you can change the representation of certain selections in the Graphics tab or highlight certain residues in the Analysis tab.
If you have any problems with VMD prior to loading VMD lite, you may consult the VMD main page. To learn more about VMD, there is a tutorial available that gives a detailed account of how to use VMD’s more complicated features.
We supply lesson modules alongside VMD lite. These lesson modules may be downloaded here. Note that to use the latest version of the module, you may need to update a file on your system; see readme.txt for more information. Alongside the lesson module there is a PDF with an accompanying lesson plan. Unzip the downloaded folder. In VMD lite, select “Load Lesson” and select the folder “lessons” (from zip file). VMD lite will automatically scan the lessons folder for all contained modules. If you only have the “Phospholipids” lesson module downloaded, you will see
Click “Load Phospholipids” to load the lesson module. You should then see a new window
Clicking “Exit” will return to the main VMD lite screen.