POLYVIEW-3D Tutorial



The following software and web-servers are being utilized and/or cross-linked by the POLYVIEW-3D web server:

  • W.L. DeLano's PyMol from DeLano Scientific, San Carlos, CA, USA and
    Roger Sayle's RasMol (v 2.7.3) from Biomolecular Structures Group, Hertfordshire, UK
    They are being used to render 3D images of macromolecular structures.
  • Jmol java applet
    It is being used to set up the initial structure orientation, center of view and zoom level.
  • The DSSP program by W. Kabsch and C. Sander available at the Centre for Molecular and Biomolecular Informatics, University of Nijmegen, Netherlands
    It is being used for calculation of the protein secondary structure and relative solvent accessibility.
  • The BLAST program from National Center for Biotechnology Information (NCBI), USA
    It is being used to perform sequence homology search and obtain multiple sequence alignment
  • The CASTp server from L. Liang lab at University of Illinois at Chicago, USA
    It is being used for finding pockets within macromolecular structure.
  • The Pfam database from Wellcome Trust Sanger Institute, UK
    It is being used to find and map known protein domains to the submitted structure.
  • The PDBTM database from the Institute of Enzymology, Budapest, Hungary
    It is being used for mapping the protein regions putatively spanning membrane to the submitted structure.
  • The ImageMagick software suite.
    It is being used for converting images into different formats and enhancing static slides with advanced graphic effects.

We would also like to thank users of POLYVIEW-3D for their feedback, and especially Prof. E. Martz for his valuable suggestions and endorsement of our efforts to improve the server.


Design and text of the tutorial was developed by A. Porollo and J. Meller

For additional information, refer to our Frequently Asked Questions.

Your feedback is very welcome.

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Last modified: Thu Feb 9 13:32:32 EST 2012

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