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university of cambridge  


   eadfrith

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Eadfrith

Eadfrith Homepage

If you want to look at a molecule quickly, without starting MacroModel type eadfrith Filename. This will display the molecule in a MacroModel file and allow you to manipulate it. You can also render the molecule to produce pictures suitable for publication, posters or the WWW, and display the normal modes of a system.

When you run eadfrith you will get the following messages:

 Use ESC key to exit, SPACE to render
 LEFTMOUSE to enlarge,
 MIDDLEMOUSE to rotate, RIGHTMOUSE to move.
 Options:
 (A) Radii: 1.000000 
 (B) Bond Option: 0
 (C) Full screen picture
 (D) Full contrast
 (E) Background colour (RGB): 0 0 0
 (F) New Orientation
 (G) No NMA
 (H) Colour option           0
            Reading Colours
 (I) No Initial Depth Cue
 (J) Line Width: 1
 (K) Ambient Light 0.5000000 
 (L) Bond radius  0.3000000
 (*) Quit
 Enter a letter, then RETURN, to alter options
 or press RETURN to continue

The first time you run the program, you may also get a message saying that it cannot find an Options file, so it will guess the options that you want. It will then create an Options file, and store any changes you make to this menu.

Press RETURN immediately to display your molecule. It will appear in a new window, and can be rotated, enlarged and moved using the mouse. A rendered version can be made by pressing the space bar. The window can be killed by pressing the ESC key (top left of the keyboard).

To alter the settings, type a letter, then press return. You may then be asked for more information. The options control the picture in the following ways:

  • A: Alter the radius of the rendered spheres (drawn when the space bar is pressed). 1.0 gives a ball and stick model; 4.0 gives a CPK model.
  • B: Controls the colouring of the rendered bonds.
  • C: Toggles between a new window and filling the screen with the molecule.
  • D: Controls the contrast in the rendered picture.
  • E: Controls the colour of the background. 0, 0, 0 gives a black background; 255, 255, 255 give a white background. The first number is the red component of the colour, the second is the green component, the final number is the blue component.
  • F: Decides whether to use the orientation of the previous molecule, or to use a new orientation.
  • G: This option enables you to animate normal mode analyses.
  • H: This switches between using standard colours, or reading them from the file.
  • I: Turns depth cueing on or off while molecules are rotated.
  • J: Determines the width (in pixels) of the lines that make up the molecule.
  • K: This figure is the ratio of ambient to directional light in the rendered figure.

Eadfrith may be downloaded from this server. Eadfrith is described in: J. M. Goodman. J. Mol. Graph. 1996, 14, 59-61. Please cite this reference if you use the program.


Pictures created by Eadfrith have been included in many publications and presentations, including:
  • Molecular Biology at Tübingen (DNA and protein)
  • Angew. Chem. 1998, issue 4, Cover Picture
  • J. Chem. Soc. Dalton 1998, issue 3, CD-Rom
  • Chemical Communications 1997, 1879
  • innovation&technology@cam.ac.uk (A publication of Cambridge University's Press Office)
  • Chemical Communications 1997, issue 6, CD-Rom
  • J. Med. Chem. 1996, 39, 1806
  • Electronic Conference on Trends in Organic Chemistry (ECTOC-1) Ed. H. S. Rzepa, C. Leach and J. M. Goodman. RSC 1996
  • Tetrahedron Asymmetry 1995, 6, 2613 (Supporting Material)
  • J. Am. Chem. Soc. 1995, 117, 9768 (Supporting Material)
  • Tetrahedron 1995, 51, 4853
  • Foundation Chemistry J Raffan and B Ratcliff, Cambridge Modular Sciences, CUP 1995
  • Statistical Mechanics, Protein Structure and Protein-Substrate Interactions Ed. S. Doniach, Plenum Press, New York. 1994

Modifications
A version of Eadfrith is being developed in Java
Preliminary Examples
Version 1.1 (July 1997)
If there is no Options file in the current directory, Eadfrith tries the $HOME directory, and then the $EADFRITH_HOME directory.

Eadfrith illuminated the Lindisfarne Gospels.



© Goodman Group, 2005-2017; privacy; last updated September 23, 2017

department of chemistry University of Cambridge