TODO - html & put on sourceforge site

GDIS Manual
===========

GDIS is a molecular modelling GUI. It was originally intended just
for loading and rotating simple models and then rendering pretty
pictures. It has grown to be much more than that.

However, the idea of loading up a model and performing various
tasks on it remains.


Models
------

The way in which you load and save models is pretty standard and can be
achieved either through the "File" menu pulldown or by clicking on the
appropriate toolbar icon.

NB: all filetype recognition is done through the extension.

GDIS can load the following filetypes:

	Biosym (msi/accelrys/whatever) .arc and .car files.
	cif (.cif)
        fdf the free data format, suitable for the SIESTA package (.fdf)
	marvin output (.mvnout, .mvout)
	gdis morphology file (.gmf)
	gulp input (.gin), restart (.res), and ouput (.got)
	xtl (.xtl)
	xyz (.xyz)
Plus, If you have babel installed,
	pdb (.pdb)
        mopac output (.out)

GDIS can save files as one of the following:
	Biosym
        cif
        fdf (free data format - suitable for the SIESTA package)
	gulp input
	gdis morphology
	xtl
	xyz

Every model has inherent properties and operations that can be
performed on it. Sometimes these are not the same for different
models (eg a surface and an isolated molecule).

The properties and other model specific manipulations you can perform
on a loaded model are found in the branches of the model subtree (the
pane to the left of the main drawing area). Other, more general
operations, such as measuring bond distances, angles, etc. are all
accessible through the menus and toolbar icons. 


Modes
-----

	All operations generally act on the currently active model.
The only exception is for certain dialogs that are associated with a
particular model(s) and no other (eg energetics). Obviously, actions
performed within these dialogs act only on the associated model, even
if it is not currently active. In such cases, the model name is usually
displayed in the dialog somewhere. 

	When a model is first loaded, it is in 'normal' mode. This
is a rotation/translation and selection mode. A newly loaded/created
model becomes the currently active model.

The active model is identified by the yellow, instead of white, frame
colour (GTK drawing mode only), and is highlighted in the model tree.

GDIS was written with a three button mouse in mind.

The left button is used for making selections. Single clicks will give
atom info as well as selecting an atom. If clicked and dragged, a box
selection is drawn. Pressing shift while doing the above appends items
to the current selection.

The middle button allows you to do translation, or zoom if shift is
clicked. 

The right button will give you rotations around two of the three axes,
with shift adding rotations around the third. Rotation in discrete
amounts can also be achieved through the model orientation spinners.


3. Selections

There is only one selection allowed per model. The atoms associated
with the current selection are identified by little yellow squares,
circles, or halos (user changeable) being drawn around the atoms.
The usual stuff, such as deleting, hiding, and cutting & pasting
can be achieved through the "Edit" menu pulldown.

Also, if the control key is held down, all rotational/translational
operations (ie via the mouse) will act on the current selection only.


4. MD initializer (RDF calc)

	This dialogue will generate a cubic lattice, with input models 
placed randomly at lattice points. It is intended to be a starting
point for liquid molecular dynamics simulations. In order to get your
solute molecules properly randomized in solution, you need to load
your solvent model first, followed by all your solute models. After
this has been done, you can then run the MD dialog and fill in the
numbers (eg cube size, number of components of solute to place etc.)
and generate a box. If you're unhappy with a particular configuration,
just keep generating random boxes until it you're satisfied.

5. VdW surfaces

6. Surface generation

7. Rendering

	GDIS doesn't actually do any of this itself. It harnesses
the power of POVRay and OpenGL in order to make pretty pictures.
Both these options are available through the display properties
dialog. In general, povray images look better than OpenGL, but
with the latter you can rotate the model on the fly.


Transformations/model editing dialog

BFDH - will get it's own "morphology" dialog

Tasks?