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MacMolecular: a program for visualization of molecular structures on the Macintosh

T D Weaver1, S A Islam, D L Weaver

  • 1Dartmouth College, Hanover, NH.

Journal of Molecular Graphics
|September 1, 1994
PubMed
Summary

MacMolecular software visualizes small- to medium-sized biomolecules, especially peptides, using various representations. This program facilitates molecular modeling and animation on Macintosh computers, enhancing structural analysis.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Accurate visualization of biomolecules is crucial for understanding their function.
  • Existing molecular graphics programs may have limitations in terms of platform compatibility or feature set.

Purpose of the Study:

  • To introduce MacMolecular, a novel software for displaying small- to medium-sized biomolecules, with a focus on peptides.
  • To provide a versatile tool for molecular visualization and analysis on Macintosh computers.

Main Methods:

  • The software supports multiple display modes including stick, ball and stick, depth-cued, and space-filling representations.
  • Input is accepted from standard Protein Data Bank (PDB) files, Cartesian coordinate files, and Kinemage files.
  • Features include customizable coloring, translation, rotation, zooming, and animation file generation.

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  • Atom bonding algorithms accommodate standard distance-based methods and sequential approaches for peptide backbone visualization.
  • Stereo viewing and the ability to write modified structures to new PDB files are supported.

    • Main Results:

    • MacMolecular offers a range of visualization options for biomolecules, particularly effective for peptide structures.
    • The program enables interactive manipulation and analysis of molecular models.
    • Generation of animation files and output of modified PDB files enhance the utility for research and presentation.

    Conclusions:

    • MacMolecular provides a powerful and flexible platform for the visualization and analysis of biomolecules on Macintosh systems.
    • Its diverse input compatibility and advanced features, including animation and stereo viewing, make it a valuable tool for structural biologists and computational chemists.