Chemical Object Test

This data type is under construction. It is presently referred to as chemical/x-* by convention. Once the correct type is decided upon and registered, then it will be used.

Here is a partial list of some of the many common molecular chemical MIME formats [1,2]:

    CML chemical test (adenosine) [chemical/x-cml]

    PDB chemical test [chemical/x-pdb]

    MOL mdl chemical test (ethambutol) [chemical/x-mdl-molfile]

    TGF chemical test [chemical/x-mdl-tgf]

    SDF mdl chemical test [chemical/x-mdl-sdf]

    RXN mdl chemical test [chemical/x-mdl-rxn]

    GAU gaussian chemical test [chemical/x-gaussian-input]

    MOP mopac chemical test [chemical/x-mopac-input]

    MMD macromodel chemical test [chemical/x-macromodel]

    KIN kinemage chemical test [chemical/x-kinemage]

    JDX jcamp chemical spectra test (polystyrene, from a BIORAD FTIR) [chemical/x-jcamp-dx]

    CHM chemdraw chemical test (Tricholomic Acid, C5H8N2O4) [chemical/x-chemdraw]

    C3D chem3d chemical test (Tricholomic Acid, C5H8N2O4) [chemical/x-chem3d]


If you can not view these, you need to install a viewer:






CambridgeSoft Corporation has an index of several thousand compounds served by chemical MIME.

The PDB format is presently the preferred chemical format since so many viewers are available for all of the platforms. It is recommended that you use PDB in your HTML documents.

You can find many more examples of PDB chemicals from the NIH ``molecules R us'' utililty, the Klotho database from the Institute for Biomedical Computing, Washington University, and the Protein Data Bank.

There is also a molecule VRML test document which uses some of the advanced VRML features. This molecule is curtesy of Omer Casher, o.casher@ic.ac.uk, Imperial College, London. This is a ``CRO PROTEIN COMPLEX WITH 20 BASE PAIR PIECE OF DNA''.

One drawback of the PDB format, and the rasmol viewer when used with the MOL format, is that stereochemistry is not maintained. This issue is being looked into. Thus, if stereochemistry is important for your data, then there is not a good generic solution at the moment (other than using 2D bitmaps).



ChemSpider: Search and share chemistry http://www.chemspider.com

Chemical structure drawing search http://www.emolecules.com

Organic chemistry portal: Chemical search http://www.organic-chemistry.org/chemicals/search.htm

Thanks to Lindsey Weiss for these links.



A list of chemistry sites is maintained by the University of Sheffield.

Additional information about TGF may be obtained from http://www.ch.ic.ac.uk/tgf/

Thanks go to Henry Rzepa and Osman Güner for the TGF example data file.

Thanks go to Bernard Blessington, B.Blessington@Brad.ac.uk, Bradford University, for his example MOL contribution of three stereoisomers of ethambutol and his extensive discussion on stereochemistry. Additional information on stereochemistry is also available. In the future, CXF or MOL will probably be the preferred formats for stereochemistry.

Additional lists of Chemical databases can be found at Rensselaer's List of Chemical Databases.

For more information on the on-going chemical discussion see the chemMIME thread at http:/www.ch.ic.ac.uk/ or the ChemMIME Home Page.

Information about MOLmol, a chemical visualizier is also available.

Information about the Chemical Markup Language, CML, is also available.

The MathMol Library contains a series of 3D molecules discussed in K-12 science textbooks.

A series of 3D VRML Models of atomic orbital




References

  1. H. S. Rzepa, B. J. Whitaker and M. J. Winter, J. Chem. Soc., Chem. Commun., 1994, 1907. (http://www.ch.ic.ac.uk/rzepa/RSC/CC/4_02963A.html)

  2. O. Casher, G. Chandramohan, M. Hargreaves, P.Murray-Rust, R. Sayle, H. S. Rzepa and B. J. Whitaker, J. Chem. Soc., Perkin Trans 2, 1995, 7. (http://www.ch.ic.ac.uk/rzepa/RSC/P2/4_05970K.html)






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If you have questions about this page, contact:
Scott D. Nelson, nelson18@llnl.gov


Last Modified: October 25, 2013

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