Structure Input Options and Usage
A Brief Tutorial

M. Krein

Structure Input:

Polymer Structures can either be drawn or selected from a drop down list.  The drop-down list affords quick access to common polymers; simply select from the list to automatically populate a polymer for analysis.

Alternatively, a polymer can be drawn in for analysis, using the JME Editor courtesy of Peter Ertl, Novartis. 
General instructions on usage are available within the Java window by clicking on the "Help" Button.

Specific to drawing a polymer for this tool,  begin by drawing the base structure of the polymer repeat unit, and leave the edges of the repeat unit undefined.

For example, polystyrene would be drawn:

Next, identify and tag the edges of the repeat unit with asterisks (*).  To do this, click the "X" atom type, and in the resulting pop-up window, type an asterisk:

Close the window, and highlight and replace the end groups of the repeat unit with asterisks.

When you are happy with this, click the "Submit Molecule" Button.

At this point, you can select a particle for calculation from the drop down menu:

When you are ready to submit, click "Process Molecule"

After processsing is completed, you will be presented with a results page, in this case, polystyrene and trimethylchlorosilane: