Graphics packages

Contact information Jay W. Ponder Biochemistry, Box 8231 Washington University Medical School 660 South Euclid Ave. 

GaussView (we used Version 2.08) is a graphic interface for use with the Gaussian ab initio program. It can be used to build molecules, set up the options in the input file, run a calculation, and display results. GaussView uses the molecule builder that was written by SemiChem, but has screens for setting up calculations that are different from those in the AMPAC GUI sold by SemiChem. 

There is a screen to set up the calculation that has menus for the most widely used functions. Many users will still need to know many of the keywords, which can be typed in. There was no default comment statement, so the input file created would not be valid if the user forgot to include a comment. A calculation can be started from the graphic interface, which will be run interactively by default. The script that larmches the calculation was not too difficult to modify for use with a job-queueing system. 

The molecular structures were rendered with good-quality shading on a blue background. Isosurfaces produced from cube files or checkpoint files also looked nice. Molecular vibrations can be animated on screen and vibrational displacement vectors displayed. The vibrational line spectrum may be displayed too, but the user has no control over the axes. There is no way to set the background color. The display can be saved using several image file formats. 

Molden (we tested Version 3.6) is a molecular display program. It can display molecular geometries read from a number of molecular file formats. Various views of the wave frmction can be displayed from the output of the Gaussian and GAMESS programs. Some functionality is available from MOPAC and AMPAC files. Conversion programs are available to import wave functions from ADF, MOLPRO, ACES H, MOLCAS, DALTON, Jaguar, and HONDO. 

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The macmolplt graphics package is designed for displaying the output of GAMESS calculations. It can display molecular structures, including an animation of reaction-path trajectories. It also may be used to visualize properties, such as the electron density, orbitals, and electrostatic potential in two or three dimensions. 

Operating system printer interface graphics package. 

Normal mode analysis provides a good example of information which is obtainable only through a theoretical calculation, since spectroscopic data does not directly indicate the specific type of nuclear motion producing each peak. Note that it is also possible to animate vibrational modes in some graphics packages. 

This exercise would be a good place to compute a charge distribution difference density between the ground stale and the first excited state, and plot it using an available graphics package. 

Many graphics packages allow for contour diagrams and surface plots. These are given above for the square of the LCAO plus combination, for any plane containing the intemuclear axis. 

Currently, KARMA is in the prototyping phase. Although the hardware is connected via the high bandwidth network, it is necessary to implement the servers for data communications. Additionally, a completely new graphics package is in development for karma. The next two steps in terms of development are the turnkey and production versions of karma. 

MR is an ensemble of techniques that aims to place and orientate an approximate molecular model in the unit cell of the crystal being studied. This will provide the starting phases needed to calculate the initial electron density map from which the protein model can be built, either manually by iterative use of reconstruction with molecular graphics packages (Jones et al., 1991) followed by refinement (Murshudov et al., 1997), or automatically if diffraction data up to 2.3 Angstroms or better are available (ARP/wARP (Perrakis et al., 2001), Solve/Resolve (Terwilliger, 2003)). 

The practices contained in this section apply to Standard Software Packages (e.g., spreadsheets, text processors, database programs, CAD systems, graphics packages, and programs for technical or scientific functions) that are considered part of a computer system. By definition, this includes noncustomized application software that has been purchased and that has not been modified. 

Figure 5.1 Examples of some of the formats used by graphics packages to display molecular models on computer screens...

The most important points regarding the use of graphics packages are ... 

Figure 1. HOMO-1 of B2H2N2, projection on YZ plane bisecting the molecule along NN direction. Plotted using PLTORB utility from GAMESS graphical package (26).

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