Technical Details
Several individuals have expressed interest in understanding how different elements of this tutorial were generated. If you have further questions, please forward any inquiries to djohnston@otterbein.edu.
Info about pmesh / tmesh surfaces
Use of the pmesh command to generate simple planes and lines will soon be superceded by the draw command (available in the latest versions of the Jmol applet). This site still uses pmesh files, but will be updated in the near future. The following descriptions are included for informational purposes.
Display of pmesh / tmesh surfaces
The pmesh command has been used to generate the representations of both the reflection planes and rotation axes. Recent versions of Jmol have extended the pmesh command, but the basic syntax of the command is:
pmesh meshID [option] "filename.pmesh"
Subsequent execution of the command pmesh [meshID] ON/OFF causes the display of the surface to be toggled on or off. Additional documentation can be found at the Jmol Interactive Scripting Documentation page.
Format of pmesh / tmesh files
The format of a pmesh file is relatively simple.
- the first line defines the number of grid points defining the surface (integer, n)
- the next n lines define the Cartesian coordinates of each of the grid points (floating point, n lines of x, y, z data points)
- the remaining lines define the surface by specifying how each point is connected to the other points in the grid (integers, groups to define m polygons)
- the first number (m) identifies the number of polygons to be defined
- the next m groups of numbers define polygons:
the first number in a group (p) defines the number of integers that follow to identify an p-1 sided polygon - the last number in a group must equal the first number to close the polygon
In this tutorial, many of the pmesh surfaces are flat rectangular planes defined by a 10 x 10 grid of points. To completely fill this mesh surface requires 9 x 9 = 81 four-sided polygons. Therefore n = 100, m = 81, and p = 5.
View example (as a text file): benzene_horz_tmesh.txt
Creation of pmesh / tmesh files
The surfaces and axes for this tutorial were generated using an Excel spreadsheet allowing both generation and rotation of appropriate surfaces. The planes were generated as fully interconnected 10 x 10 grids. The axes were generated as 12-sided cylinders. The Excel files are self-explanatory and may be downloaded using the links below.
Animations
Animations were created using XYZ files with each atom defined twice; one set of atoms fixed and the others animated. The format of the XYZ files is relatively simple: the first line defines the number of atoms (n), the next line gives the molecule name, the next n lines define the elements and x, y, and z coordinates of each atom in the molecule. This format repeats to define each frame of an animation.
View example (as a text file): ammonia_reflect_xyz.txt
For these animations, the animmode=once command is set to ensure the animation runs a single time. The script sent to the molecule separately selects, sizes, and colors the fixed and animated atoms to highlight the two sets of atoms. For some molecules, an additional dummy atom is defined at the center for illustration of an inversion center.
Two additional Excel files were created to aid in the construction of some of the animations.
Javascript controls
The Jmol.js JavaScript library (jmol.org) was used for all the molecular display control. See the Jmol Scripting page for additional examples of scripting Jmol, or refer to the Jmol Interactive Scripting Documentation page for full documentation about available scripting commands.
Browser-specific Issues
Every attempt has been made to make this tutorial compatible with as many browsers as possilbe. As of this writing (7/06), all aspects appear to work with Internet Explorer 6 (PC), Firefox 1.x (PC, Mac, Linux), and Safari (Mac).