World Index of BioMolecular Visualization Resources

Deep View / Swiss-PDBViewer Resources

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  Can Your Molecular Viewer Do This? (DeepView 4.0):
An overview listing of the capabilities of DeepView version 4.0, released in June, 2008. Also links to tutorials for DeepView.

  Constructing and Exploring Crystal Contacts:
Step by step instructions for building crystal contacts in DeepView, and then selecting and saving only the asymmetric unit plus the contacting shell of atoms. Also provides instructions on how to insert MODEL/ENDMDL records for viewing the crystal contacts in Protein Explorer. See also Protein Crystal Contacts, an illustrated introduction.

  Creating Simple animations of SwissPDB Viewer files in POV-Ray:
The purpose of this page is to provide a simple step-by-step guide for setting up a simple rotation amimation (such as the one shown at the top of the page), using Swiss PDB Viewer and POV-Ray. You will probably find that for most purposes, this is the only type of animation youi are likely to want to produce anyway - if you are interested in more complex animations then this will at least provide a starting point. The result is an animated GIF file.

If you will be happy with a RasMol rendering in your animated GIF, you may find it easier to use Andreas Bohne's animation server site PDB2MGIF.

 
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  DeepView/Swiss-PDBViewer:
This is the primary site for downloading Deep View and for documentation. DeepView (known until year 2000 as Swiss-PDBViewer) is a powerful visualization and modeling freeware program. It supports mutation, alignment, energy minimization, and homology modeling, and more!         

  Learning Biochemistry with Deep View: A Gallery of Graphics Exercises for Introductory Biochemistry:
Graphics exercises for introductory biochemistry, arranged according to typical topics in a 3rd-or 4th-year college course. These exercises provide a graphics-based supplement to the traditional end-of-chapter questions in texts and study guides. In addition, they provide appropriate follow-up for the Deep View Tutorial and its accompanying graphics assignments. Many of these exercises provide Deep View project files containing prepared staring views or multiple models for comparative analyses. Others call for downloading and studying files from the Protein Data Bank.All exercises are linked to a biochemistry topics list, which, in turn, is linked to learning strategies.  

  Molecular Graphics with Swiss PDB Viewer and POVray:
Molecular Graphics gallery containing a growing number of pictures of protein structures generated with Swiss PDB Viewer and POVray. Most pictures are of metallo-proteins. The emphasis is on the artistic renderings or 'Molecular Pornography' as Gert Vriend tends to address this type of work. Each picture is accompanied by some information on how the scene was generated. Site contains a discussion board to share information.

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  Molecular Modeling for Beginners: Tutorial for Deep View (Swiss-PdbViewer):
Full tutorial on obtaining, installing, and using Deep View. Aimed at beginners, but the advanced sections will help experienced users. Includes project assignments for testing your -- or your students' -- skills with Deep View.                          

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