Molecular modelling with MacMimic

Anders Sundin Oragnisk kemi 2 sundinKC at dna.lth.se
Mon Sep 17 06:28:00 EST 1990

MacMimic is an application for the display, construction and comparison of
molecular models in full 3-D. It runs on the Macintosh II family of
computers with a 256 colour monitor and 2 MBytes of memory.

A demo of MacMimic version 1.0 is available via anonymous ftp from
pollux.lu.se as macmimic_demo.sit.hqx. The demo has all functionalities
of MacMimic except:
The demo can not save or print documents. 
Copy and Paste only works within the demo.
MM2(87) is not included.

MacMimic is distributed by:
                             Instar Software AB
                             Research Park IDEON
                             S-22370 Lund, Sweden

The Macintosh interface.

The Macintosh interface is fully implemented. MacMimic can handle multiple
windows, and runs both under the Finder and the Multifinder. Most tools of
MacMimic are placed in palettes and are therefore convenient to use. The
standard Apple, File and Edit menus are available. Undo works on every
command that changes the structure of a model. Copy and Paste can be used
to move models between display windows or to the Scrapbook.

Making pictures.

A picture of a model can be copied from a display window to be included in
a word processing document. Printing in black and white or in colour is
available directly from MacMimic. Colour printing can be performed on any
colour printer with a Macintosh compatible printer-driver. The colours used
in printing can be customized through the Preferences dialog.

Displaying models.

MacMimic can display and handle structures with up to 32000 atoms. A large
number of molecules can be displayed simultaneously in each of the windows
of MacMimic. Molecules are displayed as stick or ball-and-stick models,
each with toggable attributes such as atom labels, atom index and stereo.
Colour is used to indicate atom type, but individual atoms or whole
structures can be painted in other colours. The 3-D impression of models is
improved by a configurable depth cueing.

Input of structures.

In addition to documents created by MacMimic, structures can be input from
the MolLib library of structures, or obtained from a database as a PDB file
(Brookhaven Protein Database file) or as an XR file (Cambridge
Crystallographic Database file). Structures can also be imported and
exported to the Macintosh applications Ball&Stick and Chem3D.

Construction of models.

MacMimic has a powerful structure editor which can create new and modify
existing models. Atom type, charge and hybridization can be set for any
atom. The bond lengths and the number of ligands are automatically
adjusted. A set of substituents is available from a palette to make instant
substitutions of any monovalent atom. The new dihedral angles and bonds are
adjusted to make a low energy conformer. Any two models can be joined
(substituted) or fused to create spiro compounds or complex ring systems.

Chiral control.
Chiral control is automatically achieved as all models are displayed and
handled in full 3-D. The Enantiomer menu command changes a selected model
to its mirror image. The Swap Substituents tool can be used to let any two
substituents of an atom switch places. This tool provides a convenient way
to switch absolute configurations (R<=>S), equatorial and axial
substituents, and cis and trans isomers (Z<=>E).

Comparison of models.
Pseudo-atoms can be placed at the geometrical center of a number of atoms,
or at the extension of a bond. Models can be compared by superimposition.
Up to eight models can be superimposed (RMS fitted) simultaneously.

Energy minimization of molecules.

The MacMimic package includes the molecular mechanics program MM2(87). The
MM2(87) User's Manual provides a detailed and authorative description of
MM2(87). All computational options (for instance dihedral drivers,
restricted motion, etc.) of MM2(87) can be accessed through an interactive
input interface. MM2(87) can be run as a background task.

sundinKC at dna.lth.se ok2aps at seldc52.bitnet Anders Sundin

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