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:
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
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.
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|
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.
There are several Mac based chemical viewers available.
|MIME type / subtype||extensions||application||type|
ChemDraw Net and ChemDraw 3D are
available as part of the ChemOffice package. You may quickly get a local copy
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
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,
firstname.lastname@example.org, 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
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
For more information on the on-going chemical discussion
see the chemMIME thread
or the ChemMIME Home Page.
Information about MOLmol,
a chemical visualizier is also available.
Information about the Chemical Markup Language,
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