This investigation that I undertook was related to exploring all possible Chemical MIME types so that we could convert them to file formats that were supported across all platforms (UNIX, Macintosh and Windows) and browsers (Netscape and Microsoft).  Besides from exploring chemical MIME types, I tried to find all possible chemical file format conversion programs that were available on the WWW.

The advantage of distributing 3-dimensional data by means of VRML scenes is that you are no longer dependent on specific hardware or software. VRML is platform-independent and browsers exist for all major platforms. In contrast to Chemical MIME (i.e. sending structure files which are visualized by molecule viewers such as RasMol) the author of a scene has full control on the appearance. All geometric primitives, color, lights, cameras are predefined, and the display style is fixed. Once a scene has been downloaded, it can be examined from all sides and even walked through.

The big disadvantage compared to Chemical MIME is that the chemical structure information is essentially lost. Only balls and cyclinders remain, no notion about atoms and bonds remains. Reconstructing semi-automatically chemical information from VRML scenes, which could be reused and whose data could be re-analysed in detail, is not easy.  (Although with the enhancements of VRML 2.0 (VRML 97) with behaviors and animations there is the ability to achieve a Java or Javascript based interface with the user that could rival those Molecular Visualization Programs.  This is at our disgression on how much effort we would want to invest in this.)  The proposal to use for example Molecular Inventor files to distribute chemical 3D information is not very helpful since these files contain no longer the normal VRML objects and cannot be visualized by standard VRML browsers.

Standard web browsers can not visualise chemical data formats, such as PDB (protein database) files.  The development of a chemical MIME standard has meant that so-called helper applications can be coupled with any web browser to allow you to view chemical data across the web.

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I    Listing of the most common Chemical MIME types for molecular visualization.
II   Installation of the MIME types to your respective Platform.
III  Overview of the Chemical Viewers that would be most useful for the EC-CSE.

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The following is a list of the most common Chemical MIME types available that are most useful to the EC-CSE,
 

 

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   Installation of the MIME types to your respective Platform.

Demonstration of Installing a certain Plug-in MIME type on different Platforms and Browser Types (Using Rasmol as an Example)

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
 
Windows:

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:
 

Macintosh:
 
 

 

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Overview of the Chemical Viewers that would be most useful for the EC-CSE
    Including Documentation, Download and Tutorials on each Plugin/Program/Application

Kinemage - Overview

A 'kinemage' (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, any point can be identified by picking it, and the change between different forms can be aninmated.

Kinemages are created from Brookhaven Protein Data Bank files using the program PREKIN. The program MAGE is used to view them. See below for information on obtaining the software and instructions.

Kinemages are proposed as a subtype of the chemical MIME standard with the specification "chemical/x-kinemage" and file extension "kin".

Viewer can be downloaded from Protein Science at (http://www.faseb.org/protein/ProSciDocs/MageInstall.html)
Kinemage protein files can be downloaded by name or by type at the above address.

Documentation - http://www.faseb.org/protein/ProSciDocs/WebBrowsers.html

Download -  http://www.faseb.org/protein/ProSciDocs/MageInstall.html

Tutorial -  http://www.bmb.psu.edu/597a/les2_2.htm

Rasmol - Overview
 
Probably the most common chemical MIME format used on the web is the PDB format which is used to describe protein (and other macro-molecule) structures. By coupling a PDB viewer, such as Rasmol, you can view PDB files that have been sent across the web. Rasmol is a freely available program for most computer systems, including the Macintosh, MS-Windows and X-Windows.

RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.  The program reads in molecular co-ordinate files and interactively displays the molecule on the screen in a variety of representations and color schemes.

Documentation -  http://www.umass.edu/microbio/rasmol/distrib/rasman.htm

Download -  http://www.umass.edu/microbio/rasmol/getras.htm

Tutorial -  http://www.umass.edu/microbio/rasmol/rastut.htm

Xmol - Overview

XMol allows researchers/students to view (on any X11 display server) 3D molecular models produced by other software packages, and to print Encapsulated PostScript copies of molecular displays. Molecular models can be translated and rotated in a
variety of ways. Animations of multi-step datafiles are possible, as are the calculations of atom-to-atom distances, bond angles, and torsion angles. Modest editing features are also supported, allowing the user to change the type and charge of individual atoms.

XMol (Version 1.5) User Guide
http://www.msc.edu/msc/docs/xmol/XMol.html
XMol Tutorial
http://www.msc.edu/msc/docs/xmol/v1.5/tutorial.html
XMol FAQ
http://www.msc.edu/msc/docs/xmol/faq.html
 
CHIME - Overview

Chime is a free program to show molecular structure in three dimensions. Its images look like RasMol's because Chime is derived, in part, from RasMol. Chime differs from RasMol in that Chime sits directly on a web page (runs inside your browser as a plug-in), whereas RasMol is a standalone program (runs outside your browser, independently).  This makes them more easily accessible than are RasMol "movie" scripts. By virtue of being embedded in web pages, Chime removes many limitations which RasMol places on educational tutorials. In addition, enhancements to RasMol's scripting language which have been implemented in Chime make it far superior to RasMol for educational scripts.  Chime also differs in that it shows only the molecule(s) provided by the author of the web page you view, whereas RasMol can show any molecule for which you have an atomic coordinate (PDB) file

Documentation -  http://www.mdli.com/download/chimedown.html

Download -  http://www.mdli.com/download/chimedown.html

Tutorial -  http://www.umass.edu/microbio/chime/index.html

CS ChemDraw

The ChemDraw plugin can function as a remote database query client - you can draw a structure and send it over the web to a remote database. The database can return the information to you as a ChemDraw structure, which you can then save to disk as a ChemDraw document , or view in your browser. Both Plugins require both Java and JavaScript. If you have either of these features disabled in your browser (some firewalls also disable these features), you will be unable to use the ChemDraw Plugin.

Documentation - http://doc.camsoft.com/ChemDraw/Help/CDPage.htm

Download -  http://www.camsoft.com/plugins/chemdraw.html

Tutorial - http://doc.camsoft.com/ChemDraw/plugintutorial/index.html
                http://copper.chem.umass.edu/Courses/CHEMISTRY265/chem/chemlink.html

CS Chem 3D

Chem3D Plugin enhances ChemDraw further - you can see and rotate 3d models in your browser window, without the need to switch to a separate application. It supports most common molecular modeling file formats.  Both Plugins require both Java and JavaScript. If you have either of these features disabled in your browser (some firewalls also disable these features), you will be unable to use the ChemDraw Plugin.

Documentation - http://doc.camsoft.com/ChemDraw/Help/CDPage.htm

Download - http://www.camsoft.com/plugins/chem3D.html

Tutorial -  http://copper.chem.umass.edu/Courses/CHEMISTRY265/chem/chemlink.html

ISIS/Draw

ISIS/Draw is a chemical drawing program that understands the fundamentals of chemistry such as valence limits, bond angles, and aromatic ring systems. This understanding enables the user to create chemical graphics intuitively, which can be inserted into documents or used to build and search databases of 2D and 3D molecules, polymers, and reactions. You can graphically represent practically any kind of chemical or polymer structures for use in reports, publications and presentations, including DNA, RNA, and amino acid sequences.

Documentation - http://www.mdli.com/download/idraw.html

Download - http://www.mdli.com/download/idraw.html

Tutorial - http://www.kncv.nl/tutorials/studs/isis/