Examples of the use of JSmol with MOPAC

Modeling geometries

Active site in Chymotrypsin, Step 2: Interesting parts of a protein can be displayed.  In this example, Ser195 has formed a tetrahedral intermediate with the peptide carbon joining Trp252 and Thr253.  Well-known features, such as the catalytic triad and the oxyanion hole can easily be seen.  By toggling individual residues all the features in chymotrypsin can be explored easily.

Editing geometries

Make a salt bridge by moving a hydrogen atom: This is the simplest editing operation - moving a single atom, then using the new coordinates to update the PDB file

Modify a residue to convert from a site from enol to keto form, then optimize the resulting geometry: A more complicated operation - moving several atoms, then writing out a small block of coordinates in PDB format that can be used for updating the PDB file.  This operation is much easier to perform if all atoms in each residue are together in the original PDB file. 

Make a covalent bond between two atoms:  Forcing two atoms together to form a covalent bond requires other atoms in the region to move.  This example is extreme, in that a covalent bond is broken and two covalent bonds are formed, and many atoms move.

Make Step 2 in the Chymotrypsin mechanism:  This is similar to the previous step, but in chymotrypsin, the serine hydrogen moves on to the imidazolium ring of His57.

Notes: Other geometric operations, such as changing one atom to another, e.g., changing a carbon atom to a nitrogen atom, or adding hydrogen atoms, should not be done using JSmol.  Instead, edit the PDB file directly, to change element names, and add hydrogen atoms using MOPAC.


Follow a normal mode of vibration: CH2O.  This example is for a time-dependent normal mode of vibration for formaldehyde.

Follow the Intrinsic Reaction Coordinate for a reaction: HCN ↔ HNC .  This is the time-independent path for the isomerization of HCN to HNC.  The most important points are the starting point, the transition state, and the finishing point for the reaction.



For JSmol commands, see: http://chemapps.stolaf.edu/jmol/docs/