.. _HTML:
``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 <../JSmol_examples/Compare%201EJG%20and%201CBN.html>`__
(`zip <../JSmol_examples/Crambin.zip>`__)
`Detail of ester hydrolysis
step <../JSmol_examples/Chymotrypsin_Step_5.html>`__ in chymotrypsin
peptide hydrolysis.
`Detail of tetrahedral
intermediate <../JSmol_examples/Chymotrypsin%20Make%20Step%202.html>`__
in chymotrypsin peptide hydrolysis.
Animation of `Diels-Alder
reaction <../JSmol_examples/Diels-Alder.html>`__ involving ethylene and
butadiene (animation only).
Animation of `Diels-Alder
reaction <../JSmol_examples/Diels-Alder_energies.html>`__ involving
ethylene and butadiene (energies and animation).
C=O stretch `vibration <../JSmol_examples/Formaldehyde_vib.html>`__ in
formaldehyde.
`HCN <=>
HNC <../JSmol_examples/HCN-HNC%20Intrinsic%20Reaction%20Coordinate.html>`__
Intrinsic Reaction Coordinate
Examples of HTML files generated by MOPAC
`Chymotrypsin <../Chymo.html>`__,
`MTH1 <../Enzyme_specificity_(2016).html>`__