Make the world go around:

Make the molecule go around:

http://www.umass.edu/microbio/rasmol/history.htm

History of Visualization of Macromolecules :

1895: W. C. Roentgen discovers X rays.1912: Max von Laue discovers X-ray diffraction by crystals.1913: W. L. Bragg reports the crystal structure of NaCl .1935: J. M. Robertson solves the structure of pthalocyanin.1948: Bijvoet solves strychnine (cryst. decides bet. alternatives).1958: Kendrew reports the crystal structure of Myoglobin.1962: M. F. Perutz and Sir J. C. Kendrew win the Nobel Prize for their studies on the structures of globlular proteins.1965: Lysozyme. 1968: Haemoglobin . 1971: Insulin.1971: PDB established at Brookhaven National Lab., NY.

The first 3D Macromolecular ModelFor the first X-ray crystallographic solution of

a macromolecule, myoglobin, Kendrew and coworkers (1958) built brass models at a scale of 5 cm/Ångstrom. The models were built and supported within 2,500 vertical rods arranged to fill a cube 2 meters on a side. Colored clips were attached to the rods to signify electron density, and guide the building of the model.The forest of rods obscured the view of the model and made it hard to adjust. Its size made it cumbersome and problematic to move.

Kendrew-style model

The Second 3D Macromolecular ModelIn the late 1960's, Richards and coworkers

introduced an optical comparator that facilitated building a Kendrew-style brass model. Electron densities resulting from crystallographic solutions were printed by computer on paper, and their contour lines were traced by connecting numbers of similar values. These contour lines were then traced onto transparent plates. The plates were mounted vertically, equally spaced, creating a sliced three dimensional electron density map. Half-silvered mirrors were arranged to superimpose the electron density map upon the brass model.

Richard’s Box

The Third 3D Macromolecular Model

Byron Rubin, while working as a crystallographer with Richardson in the early 1970's, invented a machine for bending wire to follow the backbone trace of a protein.

Byron's Bender

The small backbone wire models from Byron's Bender were the most manipulable and portable models available at the time. Byron's Bender remained available through the 1990's.

Computer Representations

The first system for the interactive display of molecular structures was devised at MIT in the mid-1960s. Taking advantage of Project MAC (Mathematics And Computation ), one of the early time-sharing mainframe computers, Levinthal and his colleagues designed a "model-building" program to work with protein structures. This program allowed the study of short-range interaction between atoms and "online manipulation" of molecular structures.

Earliest Computer Representations, 1960's - 1970's

Computer RepresentationsEarliest Computer

Representations, 1960's - 1970's The display terminal (nicknamed Kluge) was a monochrome oscilloscope, showing the structures in wireframe fashion. Three-dimensional effect was achieved by having the structure rotate constantly on the screen. Technical details of this system were published in 1968. What could be the full potential of such a set-up was not completely settled at the time, but it was paving the way for the future.

Created in FORTRAN by Carroll K. Johnson, of the Oak Ridge National Laborotory, and first released in 1965, ORTEP rapidly became a favorite of crystallographers and protein crytallographers to produce illustrations of structures for conference presentations and publications. A key strength of ORTEP was its capacity to generate stereoscopic images automatically.

1965; Oak Ridge Thermal-Ellipsoid Plot Program

ORTEP 2 was released in 1976, ORTEP 3 in 1996 and ORTEP3 for windows is available since 2000 from the official ORTEP website: http://www.chem.gla.ac.uk/~louis/software/ortep3/

1978; Frodo :

http://afmb.cnrs-mrs.fr/rubrique113.html

Frodo was originally written by Alwyn Jones in Robert Huber's group at the Max Planck Institute in Munich and ported to E&S computers. During the 1980's, FRODO was the standard electronic Richards box program.Turbo Frodo is a general purpose molecular modelling environnement aimed at people with the need to model macromolecules, polypeptides and nucleic acids. Turbo Frodo displays 3D models using various representations including Van der Waals and Connolly's molecular dot surfaces and reads and displays X-ray density maps. Frodo is also aimed at ligand fitting and protein stacking.

Turbo Frodo can interactively mutate a protein or chemically modify it, and evaluate the resulting conformational changes. Secondary structure calculation and their representation can be performed automatically.

1991; O:

http://imsb.au.dk/~mok/o/

A team led by Jones TA from Uppsala, Sweden wrote the program O, in the 1991. O is a macromolecular modelling environment. The program is aimed at scientists with a need to model, build and display macromolecules. O is mainly aimed at the field of protein crystallography, bringing into use several tools, which ease the building of models into electron density, allowing this to be done faster and more correctly.

Unlike other molecular modelling programs, O is a graphical display program built on top of a versatile database system. All molecular data is kept in this database, in a predefined datastructure.

1992; Mage:

The Richardsons described the kinemage (from kinetic image), and their supporting programs MAGE and PREKIN. By virtue of its implementation on the Macintosh, this was the first program, which brought molecular visualization to a large number of scientists, educators, and students.

http://kinemage.biochem.duke.edu/software/mage.php

1993; RasMol:Roger Sayle managed to write the second fastest

sphere-shadowing program (ray-tracing algorithm) in the world while he was a computer science undergraduate student at Imperial College. In 1990, Roger entered graduate school in computer science at Edinburgh University, where he continued to

develop his program under the mentorship of crystallographer Andrew Coulson.Roger developed his program into a complete molecular visualization system, and by 1993, it was being used in teaching and research.

http://www.umass.edu/microbio/rasmol/index2.htm

1993; RasMol:In spite of the fact that Roger’s initials are R.A.S, The

name "RasMol" is derived from Raster (the array of pixels on a computer screen) Molecules.

The fact that Roger generously placed the C language source code for RasMol in the public domain allowed others to adapt the program to additional types of computers, and to incorporate RasMol's wonderful user interface and renderings into derivative programs. Such derivatives include notably MDL's Chemscape Chime and Molecular Simulations' WebLab .

http://www.umass.edu/microbio/chime/whatis_c.htm

1996; Chime:Bryan van Vliet and Tim Maffett at MDL Information

Systems, Inc. spearheaded the development of Chime (CHemical mIME), a visualizer in the form of a Netscape Navigator plug-in. Chime uses an adaptation of the rendering and command-language from RasMol. About 16,000 lines of Sayle's source code were converted to C++, made reentrant, and built into Chime.

To this, MDL added more than 80,000 lines of original code to create Chime version 1.0. Chime was first made available as a beta pre-release in February, 1996.

Comparison1: Chime vs. RasMol:

http://www.umass.edu/microbio/chime/chimvras.htm

Both RasMol and Chime have superb graphic renderings and incredible speed. Beyond these qualities, RasMol offers a powerful and engaging interface for self-directed exploration of molecules. Chime is much more effective than RasMol for presentations of chemical structure information (see Chime vs. RasMol ). In part this is because, by operating "on the paper" of a web document (as a Netscape plugin) Chime can be surrounded by explanatory text and color keys, in part because buttons in the text can control what Chime does (via javascript or LiveConnect), and in part because new and powerful features, which go beyond RasMol, have been added to Chime.

http://molvis.sdsc.edu/protexpl/morfdoc.htm

1998; Protein Explorer :

Protein Explorer, first made available in late 1998, and continually enhanced since then, provides (in addition to a command-line interface) a user interface to Chime that enables loading any molecule through the Internet, or from your local disk. Protein Explorer's menus, buttons, and extensive automatially displayed context-sensitive help enable RasMol-like self-directed exploration without learning the extensive RasMol command language.

1996; MolMol :MOLMOL (MOLecule analysis & MOLecule display) is a molecular graphics program designed for display and analysis of macromolecules, determined by NMR. Based on the OpenGL graphics language, MOLMOL was released by the research group of Professor Kurt Wüthrich at ETH in Zurich, Switzerland.

Some of the most useful capabilities of MOLMOL are its numerous analysis like solvent-accessible surfaces calculations and production of extremely high quality molecular graphics.

http://129.132.45.141/wuthrich/software/molmol/index.html

http://www.accelrys.com/dstudio/ds_viewer/

DS Viewer/ViewerLite

Free mol. Visualization software :Protein Data Bank-Sofware-Molecular

Graphics: http://www.rcsb.org/pdb/software-list.html#Graphics

Index of Molecular Visualization Resources (by ABC): http://molvis.sdsc.edu/visres/

molvisfw/revise.jspIndex of Molecular Visualization Resources

(By subject):http://molvis.sdsc.edu/visres/index.html

Free Molecular Modelling Programs, Review:

http://www.marcsaric.de/molmod2.html