World Index of BioMolecular Visualization Resources

Inorganic/Crystal Structure Visualization Tutorials

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  CoSyM - Continuous Symmetry Measures:   (English and Hebrew )
The CoSyM website provides tools for calculating continuous symmetry measures online for any molecule given in PDB format, and uses Jmol for three-dimensional visualization.

A number, on a scale from zero to 100, describes the distance of a given structure from perfect symmetry; or how much chirality it contains; or to what extent it resembles a polyhedron. The approach to all of these questions is based on the same general principle. That general principle is translated into a computational method for measuring the degree of symmetry point groups, from which several additional specific important measures are derived: Measuring the degree of the basic symmetry elements; Measuring the degree of polyhedral shape content; Measuring the degree of chirality.

The website is suitable for researchers, teachers and students, and is part of an undergraduate course for chemistry students at the Open University of Israel.       

  Interpretation of spectra using Tanabe-Sugano diagrams:
Part of a 2nd year course on first row transition metal chemistry. Spectra displayed using CHIME and JAVA applets provided for interpretation of d2 and d3 complexes using Tanabe-Sugano diagrams. Other diagrams provided for other configurations.     

  Molecular database without transition elements:   (English and French )
Fifty files with the pdb format that describe the geometric characteristics of simple inorganic molecules. Theses files were made with the atom's coordinates to respect the experimental values. So, theses files permit the illustration of classical geometries learnt in the VSEPR method

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  Molecular Symmetry Online:   (English and Hebrew )
The Molecular Symmetry Online Website is a Chime based collection of tools that allow users to practice molecular symmetry in 3D. It contains an example window with a small database of molecules and their symmetry elements. Animations of symmetry operations made with Flash are also included. Another useful tool is an Excel based symmetry toolkit that can be downloaded to the user's computer. The toolkit is based on a JavaScript enhanced HTML window, with a Chime window, embedded in Excel. The "load pmesh" command of Chime is used to display symmetry elements. A specially designed VBA based wizard helps users to create their own symmetry elements in tmesh format. A database of over 50 molecules in molfile format is included with the toolkit, but other molecules can be loaded as well. Help files, links and short tutorial on molecular symmetry are included in the Website. The Website requires Internet Explorer 5.5 or above.   

  Oscail Tutorials:
Build and examine cubic and hexagonal diamond, rutile, anatase, brookite, quartz cristobalite and tridymite. Use coordination polyhedra to study structures using opengl graphics with high resolution hard copy. Molecular structures are displayed using Moilin.     

  Structures of Binary Salts:
Part of a 2nd year Inorganic course on first row transition metal ions. CHIME displays of spinels, CdCl2, CdI2, CrCl3 etc showing close packed arrangements found for a number of oxides and halide compounds of the transitions metal ions.

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  Structures of Inorganic Crystals:
These Chime tutorials are designed to illustrate a number of simple inorganic crystal structures. They also show coordination number and packing for the various cations and anions, and point out relationships among the different structures. Individual pages cover Elements (Cu, Zn, C, etc.), Halides (NaCl, CsCl, etc.), and Oxides (TiO2, ReO3, PbTiO3, etc.).

  Symmetry Tutorial - Chime:
This Chime-based tutorial introduces point-group symmetry elements and operations. The material is appropriate for any undergraduate course in physical chemistry, inorganic chemistry, or spectroscopy. The basic symmetry elements and operations are illustrated using a combination of molecular structures, XYZ animations, and pmesh surfaces. Display of each element is controlled through appropriate JavaScript controls.

  Symmetry Tutorial - Jmol:
This Jol-based tutorial introduces point-group symmetry elements and operations. The material is appropriate for any undergraduate course in physical chemistry, inorganic chemistry, or spectroscopy. The basic symmetry elements and operations are illustrated using a combination of molecular structures, XYZ animations, and surfaces. Display of each element is controlled through appropriate JavaScript controls.     
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  Water Simulation:
A theoretical simulation of 10 water molecules assembling into a compact, hydrogen-bonded network. Available as saved animations viewable in Chime, and as a morph for Protein Explorer. Ten questions are provided for students about the final hydrogen-bonded droplet.      
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10 total titles.
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