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Jean-Yves Sgro
Inst. for Mol.Virology
731B Bock Labs
1525 Linden Drive Madison, WI 53706

IMAGE INFORMATION

Images can be used for in-class teaching and seminar presentations.
Commercial usage is prohibited without prior authorization from the image author(s) or their repective rightful copyright owners.

Agencies:

For non-academic licensing the following independent agencies can be contacted:

X-ray Data

Unless otherwise noted images were created by Dr. Jean-Yves Sgro from published X-ray data on Silicon Graphics, Inc. (sgi) hardware with program GRASP (Graphical Representation and Analysis of Structural Properties) written by Dr. Anthony Nichols. A special depth cueing is added within GRASP to enhance the topographical aspect of the molecular surface.

Other software used for depicting X-ray data are UCSF Chimera, Rasmol, VMD and Qutemol on desktop computers (Apple Macintosh or Windows PC, see references and links below.)

Published X-ray data are available at the Protein Data Bank (now called Research Collaboratory for Structural Bioinformatics (RCSB)) and for icosahedral viruses at the VIPER (Virus Particle ExpoloreR) site.

CryoEM data

Newer entries were created with Chimera.

Reovirus images and the various images from the Encyclopedia of Virology Plus CD-ROM were created by Stephan Spencer while a student with Prof. Max Nibert (now at Harvard Medical School.) Unless otherwise noted, cryoem data files were from Tim Baker's Laboratory, Structural Virology (then at the Markey Center for Structural Biology at Purdue University, now at UCSD).

Cryo-EM images were created with radial depth cueing within program IRIS Explorer v.2.2 (Spencer et al., 1997, see below).

References

  1. Spencer SM, Sgro JY, Dryden KA, Baker TS, Nibert ML
    IRIS explorer software for radial-depth cueing reovirus particles and other macromolecular structures determined by cryoelectron microscopy and image reconstruction.
    J Struct Biol 1997 Oct; 120(1):11-21
  2. GRASP:
    Nicholls A, Sharp KA, Honig B
    Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.
    Proteins 1991;11(4):281-296
  3. PYMOL:
    DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, Palo Alto, CA, USA.
    Delano, W.L. PyMol: An Open-Source Molecular Graphics Tool. (2002). CCP4 Newsletter No 40. (html) - (pdf)
  4. UCSF - Chimera:
    Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

    UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.

  5. RASMOL:
    Roger Sayle and E. James Milner-White. "RasMol: Biomolecular graphics for all", Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374.
  6. VMD:
    Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.
  7. Qutemol:
    Marco Tarini, Paolo Cignoni, Claudio Montani: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization IEEE Transactions on Visualization and Computer Graphics Volume 12 , Issue 5 , Pages 1237-1244 , 2006 , ISSN:1077-2626
  8. Encyclopedia of Virology Plus CD-ROM. Robert G. Webster and Allan Granoff Editors. 1995 Academic Press