ARM Club 1/ARM_CLUB_CD.iso/contents/education/a/mole/!Mole/!Help/HelpText

Text File | 1993-05-19 | 19KB | 449 lines

Help on !Mole
/***************************************************************************\
*                                                                           *
*       !Mole,                                                              *
*                                                                           *
*       3D Molecular modeller,                                              *
*                                                                           *
*       version 2.00 (28-Sep-92),                                           *
*                                                                           *
*       © Simon Kilvington, 1992                                            *
*                                                                           *
\***************************************************************************/


   Mole is a program to edit and display molecular models, these may then be
saved as Sprite or Draw files, or rendered to give a more realistic 3D image
which can then be saved as a sprite.

Main menu options
=================

'Save'
   leads to a submenu which allows the saving of the current molecule as a
Mole, Sprite or Draw file. Each of these options leads to a normal 'Save as'
dialogue box.
   Note: Draw files are not clipped to the size of the main Mole window, so
if a molecule is not fully visible when the window is at full size, parts of
it will lie outside the background rectangle in the resulting Draw file.

'File'
   leads to a dialogue box giving information about the current molecule.

'Display type'
   leads to a dialogue box that allows the molecule to be shown in several
different styles, monochrome skeletal, skeletal, 'ball and stick', space
filling or as a Van der Waals surface. The dispersion of points over the VDW
surface can be specified, large values give less points but will be faster
to draw, the dispersion is actually the arc length (in pm) between adjacent
points. It also allows Hydrogen atoms to be not shown, and the atoms to be
drawn in a way that gives a more 3D feal to the image.
   Note: at present, this 'pseudo-rendered' way of displaying molecules and
the VDW surface can not be exported to Draw files.

'Colours'
   leads to a submenu that allows the background and bond colour (of mono
skeletal and 'ball and stick' models) to be altered.

'Render'
   leads to the Render submenu, this will be discussed later.

'Show Mover'
   selecting this opens the Mover window, this allows the molecule to be
rotated and translated to your hearts content.

'Show Editor'
   selecting this opens the Editor. See below.


Mover
=====

   Clicking on the arrow icons in the Mover window will change the position
and orientation of the molecule, the angle and position steps used when the
arrow icons are clicked can be altered in the Mover menu. To get the
molecule redrawn in the main window click on the 'Update' icon, or it can be
redrawn automatically when the orientation or position are changed by
selecting 'Continuous update' from the Mover menu.
   'Return to origin' on the Mover menu returns the molecule to its origin
ie translation is 0,0,0 and the rotation about each axis is also 0.
   This rotation is about the molecules internal axis, not the screen axis.
To rotate the molecule about the screen axis, select the amount to rotate
about each axis by in the 'Screen axis' part of the Mover window, then click
on update. As before, if continuous update is selected the molecule will be
automatically redrawn when you click on one of the Screen axis arrows.
   To undo the rotation about the screen axis either rotate the molecule in
the opposite direction about each axis (you will also have to do the
rotations in the reverse order, ie if you did X +45°, then Y +10°, then Z
-30°, you would have to do Z +30°, then Y -10°, and finaly X -45° to restore
the molecule to its original orientation), or select 'Reset screen axis'
from the Mover menu.
   Note: the translation of the molecule is the last step that is performed
before it is drawn, so any rotations will not effect its position. Also, the
molecule will be redrawn a lot quicker if it has not been rotated about the
screen axis at all.


Editor
======

   On opening the Editor the edit cursor will appear in the main window,
this shows the current atom (or fragment) to join to the molecule as a blue
outline. The cursor shows where it will be attatched to the molecule. This
atom or fragment can be rotated about the bond it is going to be joined to
using the 'Rotation' icons, and  when it is in the correct position it can
be joined by clicking on the large 'Join' icon.
   Clicking on any atom in the main window will cause it to become the
selected atom, this will be shown by highlighting the atom in the main
window with a blue outline and diagramatically in the Editor window, in the
'Selected atom' icon. The diagram shows what the atom is bonded to and which
of its bonds are free to connect things to. Clicking on one of the bonds in
the diagram will cause it to be the selected bond, this is the bond to which
new atoms or fragments will be joined (if the bond is not already
connected).
   Aswell as rotating the atom or fragment to join the 'Rotation' icons can
be used to rotate selected parts of the molecule. If the selected bond is
already connected then the edit cursor will just highlight the atom to which
the bond is attatched. This atom (and the atoms connected to it) can then be
rotated about the selected bond using the 'Rotation' icons.

Editor menu
===========

'Name'
   this allows the molecule name to be changed.

'Rescale'
   clicking on this option causes the molecule to be rescaled by the program
so that the molecule picture neatly fits into the main window (well, that's
the theory anyway - it works most of the time), alternatively a new scale
can be entered in the submenu.

'Recentre'
   this translates the molecule so that the mean atom coordinates are zero.

'Atoms'
   this leads to a submenu that allows the atom type to join to be selected,
the atom types to be edited, or the atom types to be saved.
   When editing an existing atom type or entering a new one the caret is
placed in the first text icon that needs to be filled in, pressing return
will move it to the next and cause 'OK' to be selected after the last entry.
The colour of the atom type can be changed by dragging the sliders (as in
the Palette utility). The 'OK' icon must be clicked on to cause the changes
to be registered with the program.

'Fragments'
   this leads to a submenu that allows the fragment to join to be selected,
the fragments to be edited, or the fragments to be saved.
   The only aspects of fragments that can be edited from here are the name,
and where on the fragment it will be joined to the molecule. To choose which
atom to join the fragment via, select it on the picture of the fragment, the
bond to join via is selected from the atom diagram in the top right of the
fragment editor window. Again 'OK' must be clicked to register the changes.

'Change atom'
   this allows the currently selected atom to be replaced by another atom
type.

'Move atom'
   this allows the currently selected atom to be moved to a new position.

'Close ring'
   selecting this will cause the currently selected bond to be joined to an
atom which it is touching. This has no effect if the bond is not touching
another atom.

'Break bond'
   breaks the selected bond.

'Delete atom'
   deletes the currently selected atom.

'Add Hydrogens'
   adds Hydrogen atoms to all empty bonds in the molecule.

'Wipe molecule'
   asks for confirmation if the molecule is unsaved, and then wipes it.


Rendering
=========

   The molecule is rendered onto the screen as follows. The observer views
the molecule along a line parallel to the +ve Z axis. 'xres' by 'yres' rays
of light are considered, these leave the observer and pass through an
imaginary grid at the focal distance in front of the observer. The grid is
of size 'aspect' by 1.0, divided into 'xres' by 'yres' holes evenly
distributed across it. The colour of the object at the bottom left hand
corner of each hole is rendered onto the screen. This colour depends on the
ambient light intensity and the intensity of the light reaching it from each
lamp. Light from individual lamps may be blocked by other objects in the
scene and this leads to shadows in the final image.
   The spread of a lamp is the angle over which its intensity is not zero.
The intensity within this range has a maximum along a line joining the
position and the target and falls off linearly with the angle away from this
line. A spread of zero means that the lamp has equal intensity in all
directions.
   Each lamps position and target coordinates are independant of the aspect
ratio, they are expressed in terms of fractions of the distance across the
imaginary grid. The observers coordinates are 0.5,0.5,-1.0, again these are
independant of the aspect ratio. This means that position and target
coordinates of 0,0,0 will be in the bottom left hand corner of the scene,
whereas coordinates of 1,1,0 will be in the top right hand corner, and +ve Z
coordinates are in the scene whereas Z coordinates of less than -1.0 are
behind the observer.

Rendering menu
==============

'Resolution'
   a standard set of resolutions are available, or a user definable one can
be selected. All resolutions are expressed in terms of X pixels by Y pixels.

'Aspect'
   this allows the aspect ratio (X/Y) of the image to be changed.

'Focal'
   a focal length of 1.0 will cause the rendered molecule to be the same
size as the molecule pictured in the main window. Increasing the focal
length will give a telephoto effect, whereas decreasing it will lead to a
wide angle view.

'Lamps'
   this allows you to add extra lamps to illuminate the molecule, or to
alter existing ones.
   Lamp details can not be saved, although they can be set in the config
file so that the program starts up with your prefered lamps each time. See
inside the directory 'Docs' in the !Mole application for details of the
config file.

'Ambient'
   this sets the ambient light level, ie the intensity of the light falling
on every object irrespective of the lamps.

'Brightness'
   this sets the overall brightness, too large a value will cause the
picture to be over exposed (ie too bright, so everything comes out white),
too small a value will cause the picture to be too dark.

'Shadows'
   if selected shadows are cast in the rendered image, if not, they won't be.

'Multi task'
   if selected you can still use the computer when it is rendering, a
dialogue box is opened to show how its going, and to allow you to pause or
quit the rendering. If not selected the hourglass will be displayed while
the rendering proceeds, this shows the percentage complete.

'Render'
   select this to start rendering when the above has all been set up to your
desired values. (The rendering may take a few minutes!)

'Stats'
   this shows a dialogue box with a list of statistics about the last image
rendered. The time taken, brightest red, green or blue component of an image
pixel etc.


Loading and saving
==================

   Mole files dragged onto the main window, or the Mole icon, are loaded as
new molecules, and any existing molecule data is overwritten.
   Mole files dragged onto the Editor will be loaded as fragments. If a
fragment of the same name already exists it is overwritten with the new
data, otherwise the new fragment is added to the end of the fragment list.
   Double clicking on a Mole file will cause it to be loaded as a new
molecule unless a molecule is already being edited, in which case it is
loaded as a fragment.
   When a new Atoms file is loaded atom types in the file with the same name
as existing atom types replace the previous data, atom types with new names
are added to the end of the atom types list.
   When a Mole file is loaded as a fragment the bond and atom to join it via
are set to the atom and bond that where selected when it was saved.
   Note: fragments can be saved from the Editor into the main window to be
edited, and molecules in the main window can be saved into the Editor as
fragments.


History
=======

v0.00 - 0.41 (7-Feb-91)

   Crap, unfinished, Basic program that only allowed you to design planar
molecules because I suddenly realised I knew nothing about vectors.


v2.00 (28-Sep-92)

   Finally got around to updating the above.


v2.01 (25-Oct-92)

   The following keyboard short cuts have been added...

cursor up/down     : rotate the molecule about its X axis
cursor left/right  : rotate the molecule about its Y axis
F1/F2              : rotate the molecule about its Z axis

shift + left/right : translate the molecule along the X axis
shift + up/down    : translate the molecule along the Y axis
shift + F1/F2      : translate the molecule along the Z axis

ctrl + up/down     : rotate about the screens X axis
ctrl + left/right  : rotate about the screens Y axis
ctrl + F1/F2       : rotate about the screens Z axis


v2.02 (8-Nov-92)

   A couple of minor bugs have been fixed. It is now not possible to join
atoms or fragments to a bond that is already occupied (!), and atoms with
coordinates that are too large for the plotting routines are now clipped off
rather than being plotted in unexpected places.


v2.03 (14-Jan-93)

   A couple of other bugs have been fixed. In the rendering of cylinders the
surface normals are now always calculated correctly, the colours used in the
main window now never get out of sync with the current mode, and it is now
possible to use Mole in hi-res modes.


v2.04 (14-Feb-93)

   An option has been added to the display types menu to allow the Van der
Waals surface of a molecule to be displayed, empty bonds can now be filled
up with Hydrogen atoms and bonds can be broken using options in the editor
menu.
   A bug that caused the program to bomb out with no warning after viewing
too many dialogue boxes after doing some rendering has been fixed.
   The rendering algorithm has been altered, the output is unchanged but the
routine now predicts which objects will be visible where, and so need only
concentrate on rendering rather than trying to calculate what can be seen at
each point. This at least doubles the speed of the rendering process, and
will give even better performance increases with larger numbers of objects
and higher resolutions. Shadows also need not be calculated, this also at
least doubles the speed.
   Unfortunately I haven't sorted out all the maths for predicting where
cylinders will appear yet, so these are still rendered at the same speed as
before. Although there is a sphere at the end of each cylinder when they are
used to model bonds, so skeletal pictures will still be rendered faster than
before.
   It's a bit disheartening when you use something like MidasPlus on an IRIS
and it renders a 1000 atom protein, at a resolution of 1280 × 1024 pixels,
in about half a minute! The trouble with Mole's renderer is that it's all
floating point maths at the moment, so it'll never be particularly fast
until either you get a maths co-processor, or I convert it to fixed point.
   By the way, if you have RISC OS 3.1 then the Shared C Library and the FP
Emulator modules are in ROM, using RMFaster to move them into RAM gives an
increase in rendering speed of about 10%.


v2.05 (17-May-93)

   A minor change of order in the scaling/perspective routines allows much
larger molecules to be displayed. This also showed up the fact that the Draw
file transfering bug is still here for large files.
   More optimization in the renderer, I've finally added the maths to
predict where cylinders will appear, this gives enormous speed increases, I
was using mono-skeletal Serotonin (25 atoms) to test the routine and the
time taken to render it, at low resolution, was reduced from just over 3
minutes to about 35 seconds (on an ARM3).
   Also, precalculation of which objects can not possibly cast shadows on
each other knocks about a third off the rendering speed. Again, at the
moment, this only applies to spheres, cylinders may look nice but they are a
right pain when it comes to trying to predict where they are.
   The bug that caused the program to bomb out after rendering was still
there for ball and stick models, this has now been fixed once and for all.


Known problems
==============

   Mole sometimes has difficulty doing RAM transfers of large Draw files to
my version of Draw (0.44), this seems to be due to Draw giving up receiving
data after one or two buffer fills (though the need for more than one buffer
fill is brought on by Mole's fairly inaccurate estimate of the length of
large Draw files). The solution (if the problem occurs) is to save the Draw
file to disc first, and then load it into Draw from there.
   I've got RISC OS 3.1 now and the problem still occurs with the new
version of Draw (0.88), but only for much larger molecules.

   If a Mole file is dragged onto the Mole icon or into the main Mole window
it will overwrite any existing molecule that is being edited, without any
warning, even if the original molecule has not been saved.


Use and copying of this program
===============================

   Mole is a 'Freeware' program, ie you can freely use and copy it as long
as all of the following files are copied (unaltered) with it:

!Mole.!Boot
      !Help.!ReadMe
            !Run
            !RunImage
            HelpText   (this file)
      !Run
      !RunImage
      !Sprites
      AtomTypes.
      Docs.Config
           FileTypes
      Fragments.
      Sprites
      Templates

   Obviously, files may be added/deleted/altered to/from/in the 'AtomTypes'
and 'Fragments' libraries, and the 'Config' file may be altered, to best
suit your needs.


Credits
=======

   The coordinates for the C60 'Bucky Ball' (actually the vertices of a
truncated icosahedron) came from an excellent desktop polyhedra drawing
program called 'WimpPoly' by K.M. Crennell, via the 'Fortran Friends'
ShareWare library. (Much as I oppose the use of Fortran!).


Postamble
=========

   For more information, about file formats etc, see files inside the 'Docs'
directory in the !Mole application.


   Any comments, suggestions, bugs or donations can be sent to:

   Simon Kilvington,
   46 Mead Road,
   Portishead,
   Bristol,
   BS20 8NY.

   or EMAIL to '[e-mail]', although I will not be there around
Christmas and Easter, during August, or after about 1995 (when my PhD will
be finished, hopefully!).

   Donations will ensure you recieve copies of updates and related programs
if/as they are written. Projects currently planned/under development include
a program to convert SMILES strings to Mole files, and a molecular dynamics
simulation that will produce movies of molecules flexing, it will also be
able to minimise structures along the trajectory so giving the preferred
conformations of Mole files, using Fourier transforms it should also be
possible to extract bond vibration frequencies.
   I have no idea when these will be finished as I don't have much time for
programming at the moment (except my PhD stuff), but I see no fundamental
reason why they should not get done eventually.

   Right, that's that done, I'm off for a smoke.
   Student life, eh, it's all go!