The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World-Wide Web information exchange

Henry S. Rzepa

Department of Chemistry, Imperial College, London, SW7 2AY. E-mail: rzepa@ic.ac.uk

Supplemental Data and Information.

Table 1. Typical Chemical MIME Media Types

Type Filename-extension DescriptionSource of Information or Display Program
chemical/x-alchemy alc Alchemy formathttp://www.camsoft.com/plugins/
chemical/x-cdx cdx ChemDraw eXchange filehttp://www.camsoft.com/plugins/
chemical/x-cif cifCrystallographic Interchange Formathttp://www.crystalmaker.co.uk/
chemical/x-chem3dc3dChem3D Format CambridgeSoft
chemical/x-cmdf cmdf CrystalMaker Data formathttp://www.crystalmaker.co.uk/
chemical/x-cml cmlChemical Markup Languagehttp://www.xml-cml.org/
chemical/x-csml csml, csmChemical Style Markup Languagehttp://www.mdli.com/
chemical/x-galactic-spc spcSPC format for spectral and chromatographic data.http://www.galactic.com/galactic/
Data/spcvue.htm
chemical/x-gaussian-input gau Gaussian Input formathttp://www.mdli.com/
chemical/x-gaussian-checkpoint fch,fchk Gaussian Checkpoint formathttp://products.camsoft.com/
chemical/x-gaussian-cube cub Gaussian Cube (Wavefunction) formathttp://www.mdli.com/
chemical/x-isostar istr, ist IsoStar Library of intermolecular interactionshttp://www.ccdc.cam.ac.uk/
chemical/x-jcamp-dx jdx, dxJCAMP Spectroscopic Data Exchange Formathttp://www.mdli.com/
chemical/x-jjc-review-surfacerv3Re_View3 Orbital Contour filesJeffrey Gosper http://www.brunel.ac.uk/depts/chem/ch241s/re_view/rv3.htm
chemical/x-jjc-review-xyzxybRe_View3 Animation filesJeffrey Gosper http://www.brunel.ac.uk/depts/chem/ch241s/re_view/rv3.htm
chemical/x-jjc-review-vibrv2, vibRe_View3 Vibration filesJeffrey Gosper http://www.brunel.ac.uk/depts/chem/ch241s/re_view/rv3.htm
chemical/x-kinemage kin Kinetic (Protein Structure) Imageshttp://www.faseb.org/protein/kinemages/
MageSoftware.html
chemical/x-mdl-molfile mol MDL Molfilehttp://www.mdli.com/
chemical/x-mdl-rxnfile rxn MDL Reaction formathttp://www.mdli.com/
chemical/x-mdl-tgf tgfMDL Transportable Graphics Formathttp://www.mdli.com/
chemical/x-macmolecule mcm MacMolecule File Formathttp://www.molvent.com/
chemical/x-macromodel-input mmd, mmodMacroModel Molecular Mechanicshttp://www.columbia.edu/cu/chemistry/
mmod/mmod.html
chemical/x-mopac-input mop MOPAC Input formathttp://www.mdli.com/
chemical/x-mopac-graph gpt MOPAC Graph formathttp://products.camsoft.com/
chemical/x-pdb pdbProtein DataBankhttp://www.mdli.com/
chemical/x-xyz xyzCo-ordinate Animation formathttp://www.mdli.com/
chemical/x-vmd vmd Visual Molecular Dynamicshttp://www.ks.uiuc.edu/Research/vmd/
chemical/x-vamas-iso14976 vms Versailles Agreement on Materials and Standardshttp://www.acolyte co uk/JISO/

Notes and References

  1. H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, Chem. Soc. Revs, 1997, 1-10; H. S. Rzepa, "The Internet as a Computational Chemistry Tool", in Encyclopaedia of Computational Chemistry, Wiley, 1998, in press.
  2. For examples of the application of chemical MIME to electronic conferencing, C. Leach and H. S. Rzepa (Eds), ECTOC-1, Royal Society of Chemistry, 1996; ECHET96, 1997; ECTOC-3, 1998. The conferences are on-line at http://www.ch.ic.ac.uk/ectoc/.
  3. An example of the use of chemical MIME to integrate a variety of chemical data types into the body of an electronic journal is the CLIC Electronic Journal Project; D. James, B. J. Whitaker, C. Hildyard, H. S. Rzepa, O. Casher, J. M. Goodman, D. Riddick and P. Murray-Rust, New. Rev. Information Networking, 1996, 61. For the project itself, see http://chemcomm.clic.ac.uk/. For details of how a "chemically enhanced" article was prepared, see O. Casher and H. S. Rzepa, in Proc. E. Conf. Trends in Organomet. Chem.: ECTOC-3 (Eds H. S. Rzepa and C. Leach), Royal Society of Chemistry, 1998. ISBN (CD-ROM) 0-85404-889-8.
  4. N. Borenstein and N. Freed, "MIME (Multipurpose Internet Mail Extensions) Part One: Mechanisms for Specifying and Describing the Format of Internet Message Bodies", Internet RFC 1521, Bellcore, Innosoft, September 1993.
  5. H. S. Rzepa, B. J. Whitaker and M. J. Winter, J. Chem. Soc., Chem. Commun., 1994, 1907; H. S. Rzepa, Comp. Networks and ISDN Systems, 1994, 27, 317-318; H. S. Rzepa, Chem. Design Auto. News, 1994, 9, 1; O. Casher, G. Chandramohan, M. Hargreaves, C. Leach, P. Murray-Rust, R. Sayle, H. S. Rzepa and B. J. Whitaker, J. Chem. Soc., Perkin Trans 2, 1995, 7; H. S. Rzepa, in "The Internet: A Guide for Chemists", Ed. S. Bachrach, American Chemical Society, 1995; M. J. Winter, H. S. Rzepa and B. J. Whitaker, Chem. Brit., 1995, 685; A. N. Davies, Spectroscopy Europe, 1996, 8, 42; H. S. Rzepa, Science Progress, 1996, 79, 97; B. J. Whitaker, H. S. Rzepa, Proc. Int. Chem. Inf. Conf. (Ed. H. Collier), 1995, 62-71; H. S. Rzepa, O. Casher and B J. Whitaker, Proc. Int. Chem. Inf. Conf. (Ed. H. Collier), 1996, 141-148; H. S. Rzepa, W. Locke, P. Murray-Rust and B. J. Whitaker in Perspect. Protein Eng. '96, (Ed. M. J. Geisow), 1996, Paper No. 19; H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, Chem. Intl., 1997, 19, 17.
  6. H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, Pure & App Chemistry, to be submitted. The latest information is available on-line at http://www.ch.ic.ac.uk/chemime/
  7. T. Maffett and B. van Vliet, MDL Information systems. URL: http://www.mdli.com/
  8. A simple test molecule is available at http://www.ch.ic.ac.uk/rzepa/jcics/molecule.pdb A site for testing an extended set of chemical MIME types is available at http://www-dsed.llnl.gov/documents/tests/chem.html
  9. This plug-in is available at http://www.ch.ic.ac.uk/rzepa/jcics/chemical10.hqx
  10. P. Murray-Rust in Proc. E. Conf. Trends in Organomet. Chem.: ECTOC-3 (Eds H. S. Rzepa and C. Leach), Royal Society of Chemistry, 1998. ISBN (CD-ROM) 0-85404-889-8. A fully working version of JUMBO is included on the CD-ROM.
  11. P. Murray-Rust and H. S. Rzepa, to be published.
  12. A. P. Tonge and H. S. Rzepa, to be published.