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:

• UNIX:

  add the following viewer entries to your mailcap file:
  

  chemical/x-pdb; rasmol -pdb %s
  chemical/x-mdl-molfile; rasmol -mdl %s
  
  chemical/x-gaussian-input; xmol -readFormat gaussin %s
  chemical/x-mopac-input; xmol -readFormat mopii %s
  
  chemical/x-macromodel; showmcromod %s     
  chemical/x-kinemage; showkin %s
  
  
  chemical/x-mdl-sdf; showsdf %s
  chemical/x-mdl-rxn; showrxn %s
  

  
  

  where rasmol and xmol are some of the many chemical viewers. Likewise, showmcromod, showsdf, showrxn, and showkin are your favorite viewers for those formats.
  

  You may quickly get a copy of RasMol2.5.tar.Z for UNIX systems. Note that this copy may not be as recent as the previous reference however.
  

  You may get copies of a Kinemage viewer is for UNIX systems, including DEC, Sun, SGI, and Linux.

  There is also a rasterizer for SGIs called Raster3D.

  There is a structural biology viewer for biomolecular systems available from the Theoretical Biophysics Group at the University of Illionois. You can quickly get a local copy of vmd.all.tar.gz but this copy may not be as current as the previous reference however.

  
  

• PCs:

  There are several Windows(TM) based chemical viewers available. If you are using Netscape, Explorer, Mosaic, or any of the other newer browsers, you can use their HelperApplications dialog box to enter this information. Just enter the MIME type, subtype, and extension in the appropriate fields.

  To set up the Chemical viewers, enter the following into the HelperApplication or ExternalViewer dialog box in your Web Browser for each chemical type that you are interested in:
  
  

  MIME type / subtype	extensions	application
  chemical/x-pdb	pdb	raswin -pdb %s
  chemical/x-mdl-molfile	mol	raswin -mdl %s
  chemical/x-mdl-tgf	tgf	isisdraw %s
  chemical/x-gaussian-input	gau
  chemical/x-mopac-input	mop	chemdraw %s
  chemical/x-macromodel	mmd
  chemical/x-jcamp-dx	jdx	jcampdx %s
  chemical/x-kinemage	kin	mage %s
  chemical/x-chemdraw	chm	chemdraw %s
  chemical/x-chem3d	c3d	chemdraw %s

  where raswin and isisdraw are some of the many chemical viewers. You may quickly get a copy of raswin.zip, or the isis draw program, draw12w.exe, and the tutorial, draw12wt.exe. Note that these copies may not be as recent as the previous references however.

  A JCamp viewer is available. You may quickly get a local copy of the old jcamp.zip (version 0.99b.8), the 32bit version jcampvw.zip (version 0.99m3) for Win3.1 w/ Win32s, Win95, or WinNT, or the 32bit Netscape plugin NPJCAMP.zip (version 0.99m3). Note that this version may not be as current as the previous reference however. Additionally, JDX examples are also available from The University of the West Indies. Thanks go to Robert Lancashire for his efforts.

  ChemDraw3D and ChemDrawNet are available from CambridgeSoft Corporation. You may quickly get a local copy of cofnet31.zip. This viewer supports numerous formats including: chemdraw, mdl-molfile, mdl-tgf, chem3d, pdb, mopac-input, and others.

  You may get copies of a Kinemage viewer is for PCs.

  A MOLfile viewer is available. Thanks go to Joe McDaniel for this reference. This viewer supports STR (their own), MOLfile, ISIS Sketch, ROSDAL formats.
  
  
  

• Mac:

  There are several Mac based chemical viewers available.
  
  
  
  

  MIME type / subtype	extensions	application	type
  chemical/x-pdb	pdb	rasmol	text
  chemical/x-mdl-molfile	mol	rasmol	mMol
  chemical/x-mdl-tgf	tgf	chemdraw
  chemical/x-gaussian-input	gau
  chemical/x-mopac-input	mop	chemdraw
  chemical/x-macromodel	mmd
  chemical/x-jcamp-dx	jdx
  chemical/x-kinemage	kin	mage
  chemical/x-chemdraw	chm	chemdraw
  chemical/x-chem3d	c3d	chemdraw

  
  
  

  rasmol is one of many chemical viewers.
  
  You may quickly get a copy of rasmac.sit.hqx for the Macintosh. Note that this copy may not be as recent as the previous reference however.

  ChemDraw Net and ChemDraw 3D are available as part of the ChemOffice package. You may quickly get a local copy of
  
  

  • chemdrawnet3.51.sea.hqx
  or
  
  • chem3dnet3.2.sea.hqx.
  
  
  

  There is also a Kinemage viewer for Macs.

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).

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

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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