				chemical2vmd

	This program lets you use the Babel interface of VMD to load
various molecular coordinate files via a web client.
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WHAT TO DO (only for Unix machines with browsers that use the .mailcap file):

0) Install VMD (http://www.ks.uiuc.edu/Research/vmd), Babel
(ftp://joplin.biosci.arizona.edu/pub/Babel/), and perl (on SGIs, this
came on the "gifts" package and should be at /usr/bin/perl).

1) Untar (and perhaps uncompress/gunzip) the latest copy of
chemical2vmd.tar, which is available via anonymous ftp to
ftp.ks.uiuc.edu in /pub/mdscope/vmd/contrib.  This will untar to its
own directory.

2) Copy the perl script (chemical2vmd) to wherever you want it (eg.,
/usr/local/bin).  Check that the first line of the script has the full
name of the correct version of perl.

3) add the following group of seven lines to the .mailcap (either
$HOME/.mailcap or the local mailcap, eg, in /usr/local/etc or
/usr/local/lib/netscape):

# This starts VMD to view various types of molecular coordinate files
chemical/x-pdb; /usr/local/bin/chemical2vmd pdb %s
chemical/x-xyz; /usr/local/bin/chemical2vmd xyz %s
chemical/x-mol; /usr/local/bin/chemical2vmd alchemy %s
chemical/x-mdl-molfile; /usr/local/bin/chemical2vmd mdlmol %s
chemical/x-macromodel;  /usr/local/bin/chemical2vmd macromodel %s
chemical/x-gaussian-input; /usr/local/bin/chemical2vmd z-matrix %s


(you may want to change the '/usr/local/bin/' to reflect your setup.)

If you want to add more types, you'll need to find the MIME type (the
part like "chemical/*") and the name VMD uses for it.  These names are
in the chemical2vmd perl script.  I would add them here, but I either
don't know the MIME type or the mapping to the name VMD uses for Babel.

  For some test sites:

Many molecule types are available from the "Chemical Object Test" page at:
  http://www-dsed.llnl.gov/documents/tests/chem.html

http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html 
  has Alchemy Mol files

http://chem.leeds.ac.uk/Project/MIME.html
  has a PDB and an XYZ file

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THE DETAILS

	When your web browser receives a document from a remote site,
it also receives some header information which describes the type of
the document.  This is known as the "MIME type".  Based on this type
data, the correct program is launched to view it.

	Molecular information is sent via the "chemical" MIME type.
Many browsers can be reconfigured to recognize these types and launch
a molecular visualization program.  On Unix machines, and for Mosaic
or Netscape, this association is made in the .mailcap file.  (For more
information on this, see
http://chem.leeds.ac.uk/Project/MIME.html.)


	VMD should not be started directly from the .mailcap since 
  1) the command line options do not load non-PDB coordinate files, and
  2) VMD creates its own text console in the background, and returns
control to the browser, which then deletes the data file.  However,
VMD hasn't had the time to read the file yet, so nothing appears.

Instead, the .mailcap should specify the program, "chemical2vmd".
This starts VMD with the right commands to load the file (via a
temporary file containing VMD text commands), and waits a while before
exiting, to give VMD a chance to read the data.



Enjoy!

						Andrew Dalke
						dalke@ks.uiuc.edu
						Jan. 5, 1996
