Energy Maps VII

Time: 5 minutes

In the last segment, we generated a sequence of conformations.  As for the rigid energy map, it's two windows.  The graph shows the relationship between the energy of the conformation and the corresponding step of the sequential search. The other is a structure of the molecule; it changes as a function of the energy position selected on the map.

At the end of the last lesson, we left two windows open.  Let's take a look.

1. If you closed both windows previously, open them:
   1. Select File|Open and navigate to your working folder.
   2. Double-click on the isoprene.map folder.
   3. Select the arrow button in the Files of type box and choose Map(*.map) from the drop-down list.
   4. Select the seqsrch.map  file.
2. Just as for the Rigid Energy map, two windows open:



1. The left window is a two-dimensional graph showing the relationship between the energy of a conformation and the corresponding step in the sequential search.
2. The right window shows the lowest-energy conformation of the isoprene molecule. 
3. There is a small spherical marker on the energy map in the left window.  It represents the energy corresponding to the structure in the right window. Click on another position on the energy map; the conformation will change.
4. You'll notice a tool palette in each window; they function just as in the workspace.
5. The rotate tool, , will rotate the map in the graph (left) window and the molecule in the right window.
3. Change the conformation.
   1. In the graph window, choose the Select tool, .
   2. Click on various points of the graph. The conformation changes.
   3. Click on a different part of the map to see another conformation.
   4. Select the arrow button in the parameter bar at the bottom of the graph window and choose Potential_E from the drop-down list.  
   5. Select the arrow button in the parameter bar at the bottom of the structure window and choose Sequence.
   6. Select the up arrow button of the parameter box in the structure window. Clicking on the button will change the position of the current conformation.  The marker on the sequence map will move and the conformation will change in the structure window. See what happens when you click on the down arrow.
4. Animate the structure.
   1. Activate the graph window by clicking anywhere in the window.
   2. Choose Edit|Animate Along Axis.
   3. Select the forward arrow button, , to animate the structure through each step of the sequential search. The small spherical marker in the graph window moves along the corresponding positions.
   4. Select the stop button, , to halt the animation at any particular conformation.
   5. Select Done to close the Animate Along Axis dialog box.
5. Display a subset of the search sequence.
   1. Choose View|Graph Attributes  
   2. Select Attributes under the X drop-down list to display the Axis Attributes dialog box.
   3. Select Range to display the Minimum and Maximum text boxes.
   4. Click the Minimum text box. Delete the default value of 1 and type 23.
   5. Click OK to close the Axis Attributes dialog box.
   6. Click OK to close the Graph Attributes dialog box.
   7. Notice how the graph in the left window is changed.
6. Chose File|Close to close both windows of the seqsrch.map file.
7. Warning!  Select No when asked if you want to save the changes to the energy.map file

This is the end of the tutorial module on energy maps.  To learn more about Conformational Searching, check the Conformational Searching Lab Exercise from the CAChe Training Workshops.

The next Tutorial Module will address "Advanced Topics" using CAChe.