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          MolyView v1.0  --  Interactive Molecular Viewer
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Colin Frayn,
Birmingham, UK
April 2006


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Contents
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(0) - Introduction
(1) - Instructions for use
(2) - Contact Details



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(0) - Introduction
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MolyView is a simple molecular visualisation tool, for use by students of
chemistry. It displays molecules in 3D, allowing you to examine and
explore the ways in which atoms interact within molecules. It contains a
powerful visual editon which allows the user to interactively modify or
create any molecule they desire.

This instructions file will talk you through the simple control system for the
program, and introduce you to a few straightforward datasets.

Please note that MolyView is not intended to provide accurate representations
of the precise atomic configurations of complex molecules - it is merely a
visualisation aid.  Bond lengths and bond angles are not accurate, in general,
and the simulation has been tweaked in order to provide a clear presentation
rather than a physically accurate model.

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(1) - Instructions for use
--------------------------

MolyView comes as a single executable file.  Attached with this file is the
basic chemistry dataset 'MolyView.ini', corresponding to the basic periodic
table. Also included are a few example molecules which the use can load and
edit, in order to get acquainted with the software.

When you run MolyView, you will be presented with the Main Control Window.
This has four menus:

File:
New - Design a new molecule
Load - Load an existing molecule
Save - Save the current molecule
Exit - Exit the program

Edit:
Rename - Rename the current molecule
Set Formula - Set the formula for the current molecule
Add New Atom - Add a new atom to the currently selected atom (or free floating if none selected)
Join Atoms - Join the two selected atoms (or increase bond strength if they are already linked)
Unjoin Atoms - Unjoin the two selected atoms (or decrease bond strength if they are double linksed or more)
Set Controls - Adjust the controls for the dynamics
Check Molecule - Make sure that this molecule is configured properly

View:
Colour Setup - Set up any of the default colours
Text Labels - Label molecules with text?
Text Size - Set the text size
Specular Highlights - Turn on/off specular highlights
Invert Colours - Invert/uninvert the colour scheme
Highlight Links - Highlight the links of the currently selected point
Squash to 2D - Squash the entire system down to 2D (for printing)
Shadows - Add volumetric shadows (which is quite slow on some systems)
Demo - Engage demo mode (spin round automatically)

Help:
About - Display 'about' message
Website - Visit the main website

In addition, there are several keyboard shortcuts:
A  - Add a new node to the currently selected node (or free floating, if none selected)
C  - Recentre the points around the currently selected node. If none selected then uses centre of mass.
D  - Switch on/off demo mode
I  - Switch on/off colour inversion
J  - Join the two selected atoms (or increase link strength if already joined)
L  - Toggle on/off delocalised electron cloud on selected atom
O  - Alter the colour for the element type of the selected atom
P  - Pause the dynamic simulation on/off
S  - Toggle shadows on/off
T  - Toggle text labels off/symbols/names
U  - Unjoin the two selected atoms (or decrease link strength if joined by a double bond or more)
+  - Increase charge of selected atom/ion
+  - Decrease charge of selected atom/ion
Del - Delete selected atom
Esc - Quit
1-9 - Shortcut to add in new atom of given atomic number, either joined to the currently selected atom or free floating

Navigation is performed mainly using the mouse:
L-click = select an atom (hold SHIFT+ for multiple select. Click background to deselect)
L-button + drag = scroll the screen
L-button select atom + drag = Move atom
R-button + drag = Rotate scene
Mousewheel = Zoom in/out
   (also '<' and '>' on keyboard)
   Speed changed by using SHIFT+ or CONTROL+
Up/Down arrows = Alter atom scale (hold SHIFT+ or CONTROL+ to alter speed)


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(2) - Contact Details
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I am always looking for suggestions for new features to add to this software,
especially from teachers of high-school chemistry.  Please get in touch at
the address below and let me know what features would be useful in future
versions.

If you have any further questions or comments about this software, please
contact me at the address below.  I promise to read every email, though I
cannot always reply.  Please forgive me if I don't write back to you, but
rest assured that I will certainly take your points into consideration.

Dr. Colin Frayn
Email : colin@frayn.net
