Load Molecule by Name - will search the NIH Cactus server and return a structure based on name or CAS ID
number
Templates - a number of common structures
Append - this will add an additional structure to one already in the JSmol window. You will need to delete two H
atoms and use the "New Bond" button to create a new bond between the two molecules before doing an optimization
Load Methane/Cyclohexane/Benzene - will load one of the molecules
Optimize Structure - will preform a MMFF geometry optimization of the existing structure
Atom Manipulation
Off - turns off individual atom manipulation
Drag Atom - allow you to move an atom followed by a optimization to generate a dirrent conformation of the
molecule
Delete Atom - deletes a single atom
Small Periodic Table of elements - allows you to change an existing atom type
Existing Bond Manipulation
Allows you to manipulate existing bonds by breaking them or changing between single double and triple bonds.
Create New Bond
Allows you to create a new bond between an exisiting molecule and one you appended.
Extras
ESP Surface - will generate an Electrostatic potential surface mapped onto the total electron density surface.
Note charges are from MMFF
Partial Atomic Charges - will display the partial atomic charge from MMFF
Save PDB file - will save your molecule in a PDB file format for download
Save MOL File - will save your molecule is a mol file foramt for download