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MOLSYS.TXT
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1992-06-15
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New features since MolSys v0.68 -----------------------------------------------
* Load and save individual molecule fragments
* Saves GEM image files
* MultiSys™ - Up to 8 independent molecule fragments at once
- Create, copy, join, break and delete fragments
- Global or individual manipulation and display
* Set ball and stick size and thickness
* New atom types - Ionized oxygen, phosphorous and sulphur
* New functional groups
- Benzene ring and phosphoric acid
* Multiple delete command
* Preliminary animation feature
- Animate from disk or from memory
* Installation program
- Set default values and atom display types
* Calculate van der Waals energy
* Find minimum conformational energy
* Display van der Waals and covalent surfaces
* Display fragment names
-------------------------------------------------------------------------------
Preliminary Manual for MolSys v0.73
-------------------------------------------------------------------------------
© June 1992 Helion Graphics. Written by Robert Mellish & Howard Jones.
MolSys v0.73 is shareware and may not be distributed for profit or without
this text file. All source code, text files and file formats remain
copyright Helion Graphics. The programmers make no claim for accuracy or
fitness of purpose for MolSys or any of its related files and documentation.
About MolSys ------------------------------------------------------------------
MolSys is a molecular modelling package for the Atari ST. It requires a
mono monitor but should run irrespective of memory size. It was developed
from MolView v2.5, MolBuild v0.7 and MolScript v0.1. These programs were
inspired by a PC program written by Alan Mynett and published in the
October 1987 edition of Personal Computer World.
MolSys is powerful, but quick and easy to learn and use, and is capable of
directly printing output or producing files which may be imported into DTP
packages for inclusion in documents.
MolSys was written using the Lattice C V5 development package from HiSoft.
Limitations of Version 0.73 ---------------------------------------------------
MolSys v0.73 contains only a limited animation function, and is also limited to
a maximum of 100 atoms and 16 molecule fragments in memory at one time. To
register for the latest version of MolSys, see the section at the end of this
file. Please register if you like MolSys, and especially if you intend to use
it for any serious work. Registering will encourage me to produce future
versions with more features.
Changes From Previous Versions ------------------------------------------------
If you have used MolSys before, it will be necessary to re-install MolSys as
the format of the MOLSYS.INF file has changed. More importantly, the format
of MLS (molecule fragment) files has also changed, and so it is necessary to
convert any you have made with previous versions of MolSys into the new format.
This can be done with the supplied program MS_4_5.TTP. See its accompaning text
file for instructions.
Installing MolSys -------------------------------------------------------------
Configuration of MolSys is done via the MOLSYS.INF file. This file is best
edited by using the supplied installation program, MSI. The supplied INF
file should allow you to run MolSys without need for further installation.
Just double click on MOLSYS.PRG to begin. If you later want to adapt the
installation, follow the instructions below.
You should first copy the MOLSYS.PRG, MOLSYS.RSC, MOLSYS.INF, SYSTEM.FNT,
MSI.PRG and MSI.RSC into the same folder, then double click on MSI.PRG.
After the credit dialogue, you are presented with a menu which allows
you to access a series of dialogue boxes containing options and default
values which you may change.
The first dialogue is the main options. The first editable field is the
file path of the resource file. Normally, this will just be '\', which
will cause the program to search in the current directory. Note that if
the resource file cannot be found, the program will abort.
The second field is the file path and name of the 16x8 screen font to be used
by MolSys. (Usually 'SYSTEM.FNT'). This path and name will also be used when
MolSys loads the replacement 8x8 screen font, but with the extender '.FN8'
substituted (i.e. 'SYSTEM.FN8'). These are optional, and the replacement fonts
will not be used if the 'disabled' button is highlighted. These fonts are
Harlekin format screen fonts.
The third field is the default path of the molecule fragment files.
The forth field is maximum number of atoms which may be added to the
molecule. In this version of MolSys, this number cannot be set greater
than 100. If you register, you will receive a version where the maximum
number of atoms is limited only by available memory. On a 'clean' 520ST
this value can be up to about 3000, which should be adequate for most
purposes. By decreasing this number, it is possible to make more memory
available for animation, ramdisks, print spoolers, desk accessories etc.
The second dialogue is the default values dialogue. This allows the setting
of the default translation distance, rotation angle, zoom level, size of
spheres in reduced size mode and size of sticks in stickmode 3 (thick).
The third dialogue allows the setting of the type of shading used to display
the various atom types. Clicking on an atom displays the type of shading used.
Click on a shading type to change the display of the selected atom type to
that shade. Note their are two other options which can be changed, 'Colour
Shade' and 'Colour', which control the display of atoms for the colour version
of MolSys. As the colour version is not yet available, these options currently
have no effect.
Clicking on 'Save and Exit' saves the MOLSYS.INF file and exits the program.
Clicking on just 'Exit' exits without saving the file.
Running MolSys ----------------------------------------------------------------
The file MOLSYS.INF should be in the current directory when MOLSYS.PRG
is run, i.e. in the same directory as MOLSYS.PRG. On running, the program will
attempt to load MOLSYS.INF and the resource file. If these files cannot be
found the program will abort. It will then attempt to load the fonts, and then
allocate memory for screen buffers and variables. If the program runs out of
memory on loading, try decreasing the maximum number of atoms set.
Overview of Terms Used in MolSys ----------------------------------------------
In MolSys, a molecule consists of a number of sites and atoms. Atoms are shown
by their chemical symbol (e.g. C,H,O,Cl etc.) and sites are shown by a number
between 0 and 3. Sites are the only place where atoms may be placed. The type
of site shows the type of atoms which may be placed there, 0 means all atoms,
and 1,2 or 3 means only singly, doubly or triply bonded atoms. One of these
sites or atoms will be the current (or marked) site or atom. In build mode,
this site or atom will have a diamond-shaped marker placed around it. If
stick mode is on, bonds between sites and atoms are shown by lines.
A collection of sites and atoms bonded together forms a molecule fragment.
The fragments currently in memory can be shown on the fragment selector
(see below), where the visibility of fragments can be turned on or off.
One of these fragments will be the current fragment, and its title will appear
at the top of the display. Note that the current fragment does not necessarily
have to contain the current atom. The current fragment is the one on which
normally all manipulations are made.
Throughout MolSys, all distances are expressed in nanometres (1E-9 metres),
and all angles in degrees.
Selecting Functions in MolSys ------------------------------------------------
When a function icon is selected (or the corresponding keyboard shortcut is
pressed), the icon may invert, which means that further input is required.
For functions such as the freehand rotate and move controls, the mouse cursor
will change to an open hand, and the mouse moved to manipulate the