Note
This website is presently under development. The primary website for MOPAC is still http://openmopac.net until the majority of its contents have been migrated here.
HTML¶
When HTML is present a simple web-page will be written. This
web-page is intended for use with the Graphical-User Interface
JSmol, the successor to
Jmol. To suppress printing of the residue sequence, use
HTML(NORES). If charges are calculated, these will be put in
columns 62-66 of the PDB file written by keyword HTML, and these
will be available in the web-page.
Proteins are large, complicated organic compounds, and visualizing them
is difficult. There are many good GUI’s, one of which is JSmol; JSmol
allows fine control over the display of features in a protein. The
web-page written by MOPAC when HTML is present uses JSmol to display
the protein. JSmol allows simple editing of structures.
Animations¶
Two different modes are provided for showing animations.
Animations with one graph showing the molecule and next to it another graph showing the energy profile.¶
Use keyword HTML plus keywords that produce a set of frames, e.g.,
IRC, DRC, STEP, etc., but do NOT use keyword PRBOUT.
Animations with a graph showing the system in PDB format with the option to show charges.¶
Use keywords HTML and PRBOUT plus keywords that produce a set of
frames, e.g., IRC, DRC, STEP, etc.
For several examples, see Animations.
Requirements for displaying and editing a protein using JSmol¶
The JSmol software must be present. The files and folders needed for using JSmol with MOPAC can be downloaded from the latest Jmol distribution. This involves downloading a file with a name like “Jmol-14.0.13-binary.zip” Open the ZIP file, and select jsmol.zip. Extract the folder in jsmol.zip. By default, JSmol will be put into a folder called “jsmol”. Then follow the instructions in HTTP://OpenMOPAC.net/Manual/README_for_JSmol.html.
Prepare a MOPAC data set for the protein. The name of the data set will be used for both the HTML file and for the PDB file that MOPAC will make. For this description, let the name of the data set be “test.mop” Edit the data set to add keywords “0SCF HTML” The next line, a user-controlled text line, should have the title of the web-page, e.g. “Chymotrypsin” Run “test.mop” using MOPAC, this will create some files, including “test.html” and “test.pdb” At this point, have a quick look at these files using a text editor, they should look like a normal HTML and a normal PDB file.
Copy the files “test.html” and “test.pdb” into the folder “jsmol”, then open “test.html” using Firefox (other browsers - Internet Explorer and Chrome were tested - they didn’t work!). Once everything works, use the instructions in HTTP://OpenMOPAC.net/Manual/README_for_JSmol.html to modify Firefox so you don’t need to copy the HTML and PDB files into the jsmol folder - this will make running the HTML files much easier.
Displaying parts of the protein¶
The first JSmol picture is that of the entire protein. This is too complicated to be of any use, so click on “Toggle display all” - this will delete everything. Clicking “Toggle display all” again will put everything back. Start with everything deleted, i.e., an empty picture. Now look at the list of residues. Clicking on a residue will display it, clicking on it again will delete it. Build up the part of the protein you are interested in.
The other controls are easy to use.
Examples:¶
Comparison of two PDB structures for Crambin (zip)
Detail of ester hydrolysis step in chymotrypsin peptide hydrolysis.
Detail of tetrahedral intermediate in chymotrypsin peptide hydrolysis.
Animation of Diels-Alder reaction involving ethylene and butadiene (animation only).
Animation of Diels-Alder reaction involving ethylene and butadiene (energies and animation).
C=O stretch vibration in formaldehyde.
HCN <=> HNC Intrinsic Reaction Coordinate
Examples of HTML files generated by MOPAC Chymotrypsin, MTH1