Sandbox1742

This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.

Representations

The default representation is called . Be sure to click on the green text to view this default view of the 5 water molecules!

Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:

, , and .

Measuring Distances Between Atoms

Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules. Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms follow these steps:

• You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).
• Put your cursor in the structure window.
• Decide on two atoms for which you would like to measure the distance between them.
• Using your cursor, hover over one atom and double-click on that first atom.
• Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.

• Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.