WebMol - Java PDB Viewer

Author: Dr Dirk Walther
        European Molecular Biology Laboratory (EMBL), 
        Heidelberg
        Meyerhofstrasse 1
        Germany
        walther@embl-heidelberg.de

WebMol was designed to display and analyse structural information contained in the Brookhaven Protein Data Bank (PDB).

Features include:

wireframe representation of structures with full atomic detail
different color coding schemes
- atom type
- secondary structure (if defined in PDB)
- B-factor
- chain
side-by-side stereo view with adjustable separation of the images
mouse driven zoom, translate and drawing slab manipulations
selecting focus; i.e. setting point of rotation to a desired position
distance measurements
distance matrix plot and residue-residue identity plot
Ramachandran plot
dot surface
numerical calculation of solvent accessible surface area

Input options and examples:

from file (currently, under appletviewer only) http://www.embl-heidelberg.de/~walther/JAVA/example_file.html
via WWW (using URL as path to the pdb-structure) http://www.embl-heidelberg.de/~walther/JAVA/example_URL.html
via html-text file (pdb file contained as a text string in the html-file) http://www.embl-heidelberg.de/~walther/JAVA/example_HTML.html
copy and paste of PDB files or selected parts into the applet

Example html-file:

	
<html>
<body>
<!-- REMOVE codebase line when you load WebMol from a local source>
<applet code="proteinViewer.class"
   codebase="http://www.embl-heidelberg.de/~walther/JAVA/"   // with this line you get the classes 
        						     // from the specified server
           width=700 height=500>         // adjusts the size of the applet

         <PARAM NAME="PROTEIN"           // pdb identifier
	  VALUE="1kes"            
	 >
	
	 <PARAM NAME="PATH"              // file path 
	  VALUE="./"                     // e.g. current directory
	  >
	<PARAM NAME="URL"                // default URL, e.g. http://www.embl-heidelberg.de/~walther/JAVA/pdb/
	  VALUE=""
	>
	<PARAM NAME="EXT"		 // default pdb file extension
	 VALUE="brk"
	>
	<PARAM NAME="PDB_STRING"         // pdb file parsed into the html-file directly 
         VALUE=""                        // copy and paste pdb text into the quotes here
	>
</applet>

</body>
</html>

Further help is provided by the applet itself (Help button).

Beware: Macs were observed to behave inconsistently.
In particular, creating a Ramachandran and Distance Matrix plot was observed to fail.

Please send suggestions and any error messages (Java Console window) to walther@embl-heidelberg.de

Heidelberg, November 1996