Gopenmol

From MarcsHomepage

Introduction

For technical reasons, this page is names "Gopenmol", but the program is correctly named "gOpenMol".

gOpenMol is a viewer/editor-program, which has been developed by Leif Laaksonen and his group in Espoo, Finland. The first version has been released recently, and can be downloaded from the gOpenMol. The program can be run on multiple platforms, due to the fact, that it has been written with high portability in mind (the interface is based on Tcl/Tk, the graphics are generated by OpenGL).
Currently, gOpenMol is available for Windows and several Unix-flavours (executables only, no source-code).

Because it is OpenGL-based, the image quality is very good, and you can take high-quality screenshots with it.

User Interface

Gopenmol1.jpg

The user-interface of gOpenMol consists of 2 main windows, one for molecule display, and one for menu-interaction.

The program is fully menu-driven, no command language has to be learned (OK at last, you have to type in atom or group-selection, but that isn´t too hard).

Due to the fact, that the gOpenMol GUI is split into different windows, the screen becomes cluttered with menus and dialog-boxes very quickly -imho this is a disadvantage compared to a clean, flat interface with only one main window. I don´t know whether this is a result of using Tcl/Tk or if the authors preferred a more flexible arrangement of GUI-items over a more or less fixed "single-window-approach". I for my part prefer the latter. Anyway, gOpenMol is quite handy and easy to use, it has a integrated help-system (Tcl/Tk-based) and some features seem to be unique compared to the other programs in my review (the ability to load and display trajectories from various MD-packages).

Features

Display

  • Wireframe. Ball-and-stick, CPK, Ribbons, Surfaces
  • Colour scales for different purposes
  • Individual colouring of atoms and subsets
  • Plotting of labels and various results (RMSD, force-vectors)
  • Shading and lighting (OpenGL-quality)
  • 3D-2D-conversion for molecule display (for schematic display??).
  • Display of electron-density orbitals
  • Display of arbitrary cutplanes

Input/Output

  • Reads Coordinate data for Amber, Charmm, Frame Gaussian, Gromos96, gOpenMol, Hyperchem, Insight, Mol2, Mopac, Mumod, OpenMol, PDB, UHBD, Tinker, User, Xmol, XYZ, YASP.
  • Writes Coordinate data for Charmm, Openmol, PDB, Tinker, UHBD, User, XYZ
  • Reads Trajectory data (from EM/MD-packages) for Amber, Cerius2, Charmm, Discover, Gromos, Gromos96A, Hyperchem, Mumod, Tinker, Xmol, Xplor, Yasp
  • Outputs of image-hardcopies in BMP, PS, RGB, TGA and XWD format.

Calculation/Analysis

  • Measuring and display of distances and angles
  • Calculation of correlations between time-series
  • Display of trajectories
  • Calculation and display of RMSD-values over MD-trajectories
  • H-bond and S-S-bond calculation

Editing

  • Adding/deleting of bonds
  • Rotation and translation of molecules/subsets
  • Superimposing of molecules/subsets
  • Copy/Paste
  • Tcl-scripting

I haven´t checked all functions and features yet, and the list displayed above is far from being complete. It´s what I have found out after the first survey of the program. See the gOpenMol-homepage for a comprehensive list and some more explanation of the functions.