Dirk Walther

University of California,
San Francisco (UCSF)
Department of Cellular and Molecular Pharmacology,
San Francisco, CA 94143-0450
USA
phone: (415) 502 5650 fax: (415) 476 6515
email: walther@cmpharm.ucsf.edu
URL: http://www.cmpharm.ucsf.edu/~walther/

Reference:
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Walther D. (1997) WebMol - a Java based PDB viewer.
Trends Biochem Sci, 22: 274-275

Availability:
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CGI interface/ WebMol home: http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl
WebMol API: http://www.cmpharm.ucsf.edu/~walther/webmol
To download WebMol, please fill out the Academic License request form.
For installation instructions see the ReadMe.

Graphical features include:
-------------------------
- wireframe representation of structures with full atomic detail
- different color coding schemes
    * atom type
    * secondary structure
    * B-factor
    * chain
    * burial state
    * sequence conservation according to HSSP
- 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
- selecting residues according to type or burial state and regions within proteins
- animations of rocking motions with adjustable angular range
- variable background colors
 

Tools
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- distance, angle, dihedral angle measurements
- detection of steric conflicts
- peptide bond planarity analysis
- interactive distance matrix plot and other 2D-projection plots
- interactive Ramachandran plot
- dot surface
- numerical calculation of solvent accessible, van der Waals surface area, and volume
- detection of cavities
- axes assignments for secondary structural elements
- secondary structural element packing analysis
- hydrophobic moment vectors of secodary structural elements
- mainchain-mainchain hydrogen bond detection
 

Input options
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- URL, ftp, file, text string
- Format: PDB

Output options
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- Postscript