To run WebMol as a stand-alone application - allowing you to read directly
from your local file system - you need the Java runtime execution environment.
 

UNIX systems:

1) Download the file.
2) Uncompress with: uncompress webmol.tar.Z
3) Un-tar the file: tar -xvf webmol.tar

PCs/ Win95:

1) Save link as File (right mouse button)
2) Uncompress and Un-tar with WinZip

Setup:

Add the newly created webmol directory to your CLASSPATH
(e.g. setenv CLASSPATH path_to_webmol_directory or
setenv CLASSPATH path_to_webmol_dir:other_paths_separated_by_colons
or run WebMol from within the webmol directory.

Run WebMol with:

java webmol pdb_file or
java webmol http-address
(Example: java webmol http://www.embl-heidelberg.de/~walther/JAVA/pdb/1crn.brk)
or
java webmol ftp-address
(Example: java webmol ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/pdb1crn.ent )
reads the protein directly from the PDB.

Make sure java and associated programs (e.g.javat) are in you path.

NOTE: Due to some setup problem within Netscape, running WebMol over the WWW
served from UCSF or other places will no longer work properly. The reason is that
Netscape then looks up WebMol from your CLASSPATH which will cause security
violations. Fix: Unset the classpath, then launch the browser..(I know, it sucks!)

 If available (SGI), you can apply the following optimization:

1) Translate the byte-code into machine dependent optimized code: javat *.class
2) run with: java -tran -jit webmol pdb_file

Note: Resizing problems have been noticed with JDK 1.0.

Development and testing performed on an SGI running under IRIX 6.2.
Get the JDK 1.1.2 for Irix 5.3, 6.2, 6.3, and 6.4 here.