Methods, Acknowledgements and References



Atomic Coordinate Files

    1. The protein and water molecules were deleted from the PDB file, speeding up the rotation frames/second (by about 6-fold in MDL Chime).
    2. The end base pairs were remarked-out so as to produce 3' hydroxyl's and 5' phosphates on the ends, leaving 17 base pairs in 1D66-PWZ.PDB.

(Another approach would be to use theoretically-generated atomic coordinate files. These can be generated for any specified sequence, in A- or B-form DNA or A-form RNA, at Pittsburgh Supercomputer Center Web Tools. Although Eric Martz did not know about this resource in 1996 when the nonlinear tutorial on DNA was implemented, he likes the "real world" irregularities in the empirical 1D66 structure.)



Thanks to MDLI (now Elsevier MDL) for donating Chime to the world.

Thanks to Tim Maffett at MDLI for making script-enhanced Chime available during its development.

Thanks to Roger Sayle who pioneered the molecular structure rendering methods in RasMol, and whose source code was used in the development of Chime.

Thanks to the Jmol Development Team for creating Jmol, for offering it under open source and for their altruistic work and continuous improvements.

Contents and Design

Prof. Anne Simon suggested the page on ends and antiparallelism.

Dr. Frieda Reichsman ( made several good suggestions adopted in version 2.8, and caught several bugs.

The unique "MoveTo" utility server for Chime by Todd A. Carlson and Clark Wells was invaluable in scripting the zooms from the double helix to single base pairs, and back.

Jmol version was built upon the scripts and internal documentation authored by Prof. Martz in the Chime version.

Both Dr. Frieda Reichsman, Prof. Eric Martz and Dr. Gonzalo Claros (Univ. of Málaga in Spain) tested the Jmol versions, caught bugs and suggested improvements.

Dr. Anne B. Hodgson (University of York, UK) suggested improvements in the strands and helical backbone page, adopted in version 4.2.



The structure 1D66.PDB [PDB entry], from which the DNA coordinates were excerpted, was determined by:
R. Marmorstein, M. Carey, M. Ptashne, and S.C. Harrison; DNA recognition by Gal4: Structure of a protein/DNA complex. Nature 356:408, 1992 [Medline entry].

Original methods page for the MDL Chime version of this tutorial, maintained by Eric Martz.

RasMol (freeware)

OpenRasMol (freeware, GNU GPL)

MDL Chime (freeware)

Jmol (freeware, open source, GNU LGPL)

WebLab Viewer Lite, by Molecular Simulations Inc. -- discontinued; substituted by DS Visualizer

Accelrys Discovery Studio Visualizer (freeware)

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