Wanted: Mac Program visualizing PDB structures

Dan Jacobson danj at welchgate.welch.jhu.edu
Mon Jan 25 10:28:07 EST 1993


In article <ralf.727955432 at frege> ralf at frege.gmd.de (Ralf Zimmer) writes:
>I am looking for an Apple Macintosh program which displays
>3D Molecular structures. 
>I know of MacMolecule from the University of Arizona 
>(Myers/Blanco/Hallick/Jahnke).
>I am especially interested in a PDB interface, and I would be happy
>if the program allows for scaling, translation and rotation of
>3D structures (It would be GREAT if the program includes some
>PDB specific editing features ...).
>

A quick gopher search tells me that you might be interested in Macmimic - 
Demo versions are available from (among other places)

Host fly.bio.indiana.edu

    Location: /chemistry/mac
           FILE -rw-r--r--     238145  Nov 17 1991  macmimic-demo.hqx
           FILE -rw-r--r--       3672  Dec 17 1991  macmimic-demo.readme


Host ra.nrl.navy.mil

    Location: /MacSciTech/chem
           FILE -rw-r--r--     220055  May 28 1992  macmimic2.0.cpt.hqx
           FILE -rw-r--r--        713  May 28 1992  macmimic2.0.readme

A brief description clipped from the Readme file is appended to the end
of this post.

Best of luck,


Dan Jacobson

danj at welchgate.welch.jhu.edu

Johns Hopkins University


=========================================================================


This is a demo of MacMimic version 2.0 as a BinHexed self-extracting archive.
MacMimic is a molecular modeling application for displaying, building and
comparing molecular structures. An authentic implementation of the state
of the art molecular mechanics program MM2(91) is included.
MacMimic runs on Macintosh II and Macintosh Quadra computers and is de
signed
for a 256 color monitor. An FPU and 32-bit Quickdraw is required.
MacMimic is System 7 friendly and has extensive Balloon Help. Balloon Help
is only available with System Software version 7.

The MacMimic demo is the same as the full version with the following
exceptions:
The demo does not include MM2(91) and it can only Save, Copy and Print
structures with a total of ten atoms.

You may find the demo useful for exploring molecular surfaces as dot surfaces,
or for visualizing PDB files (Brookhaven Protein Database).

The author of MacMimic is Anders Sundin.
sundinKC at dna.lth.se
ok2aps at gemini.ldc.lu.se

- - - version 1 readme - - -

Molecular modeling with MacMimic.
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.

The Macintosh interface.
The Macintosh interface is fully implemented. 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.
Printing in b&w or in colour can be done directly from MacMimic, or a
picture of a model can be copied from a display window to be included
in a word processing document.

The display of models.
MacMimic can display and handle structures with up to 32000 atoms. A
large number of models can be displayed simultaneously in each of the
windows of MacMimic. Models are displayed as stick or ball-and-stick
models, each with toggable attr.
ibutes 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.

The 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).

The construction of models.
MacMimic has a powerful structure editor which can modify existing
models or create new ones. 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 (locally) low energy
conformer. Any two models can be joined (substituted) or fused to
create spiro compounds or complex ring systems.

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

The energy minimization of models.
The MacMimic package includes the molecular mechanics program 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.




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