Prepi

From MarcsHomepage

Introduction

Prepi is a GL(Silicon Graphics)-based molecular modelling package written by Dr. Suhail A. Islam at the Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, GB. Prepi stands for P rotein REP resentations I nteractivly. It comes with many functions and a powerful menu-based user interface (partly alpha-stage at the moment of course). It is available for SGI-systems (IRIX 4 and up) only, and it is free for academic use.

User Interface

Prepi1.jpg

The program consists of a main window with fixed size (which can be switched between full screen-mode and windowed mode) which contains several pull down-menus and a menu-bar on the right side.
Apparently the prog runs faster when in full screen-mode (on an Indigo2 R4400), and the fixed-size-window isn´t a good idea imho (all other programs nowadays have resizeable windows, so this feature is a bit outdated.
The program can input data from a wide range of data file formats (e.g. Brookhaven PDB, Cambridge Databank, SYBIL, Z-MATRIX) including its own FREE FORMAT which allows for the construction of complex objects such as Virus particles.

The author claims that he plans to port the program to other platforms using the XWindow-System and OpenGl. Nothing has happened in this direction, so this project can be considered pretty dead.

Features

Taken from the Prepi-homepage:

  • Liquorice and Ball & Stick display of bonds
  • Ribbons: Standard (Richardson) & Cylindrical
  • Cylinders & Arrows (to represent Helices and Sheets)
  • Spheres (to represent atoms)
  • Hydrogen Bonds & Disulphide bonds representations
  • Inertial (and Thermal) Ellipsoids
  • 2D sections through molecule
  • Planes: Disk Representations of ring structures (e.g. Heme, Tyrosine, G)
  • DNA representations (ladders)
  • Molecular Surfaces
  • Geometrical calculations
    • distances , angles and torsion angles
    • secondary structure element calculations(e.g.helix pitch)
  • Bond / Fragment rotations and translations
  • Plots e.g. Phi-Psi
  • Various NMR representations (e.g. inertial displacement ellipsoids)
  • Postscript files of cartoons e.g. ribbons, arrows & cylinders (by use of the standalone program PREPIPS)
  • Least squares surface fitting of Lines, Planes, Conics and Quadrics
  • Input File formats
    • BROOKHAVEN PDB FORMAT FILE
    • CAMBRIDGE CSD FORMAT FILE [FDAT]
    • PREPI FREE FORMAT FILE
    • ALCHEMY (TRIPOS ASSOCIATES) [FREE FORMAT]
    • CS CHEM3D CARTESIAN FORMAT FILE
    • MDL MolFile (MDL MACCS-II) FORMAT FILE
    • MACROMODEL STRUCTURES FILE (COLUMBIA UNIVERSITY)
    • MSI MOLFILE (MOLECULAR SIMULATIONS, INC)
    • SMD FILE (H.Bebak AV-IM-AM Bayer AG)
    • SYBYL MOL OR MOL2 FILE (TRIPOS ASSOCIATES)
    • MOPAC INTERNAL COORDINATES FLE FORMAT
    • INTERNAL COORDINATES FLE FORMAT
  • Interactive change of colours & material properties
  • Use of up to 6 Lights of varying colours
  • Control of background colours
  • Captions (Text, Arrows & Lines)
  • Interactive image capture (still/movie)
  • Non-graphical Computations/functions:
    • Hydrogen atom generation
    • Torsion angle generation
    • crystallographic symmetry generation of molecules
    • Residue / side-chain generation
    • Secondary Structure assignment
    • Computation of Inertial tensors
    • Data filtering