Graphical interface

D.R. Stampf, C.E. Felser and J.L. Sussman, PDBBrowse - a graphics interface to the Brookhaven Protein Data Bank, Nature 374 (1995), 572-574. 

The disadvantage of molecular mechanics is that there are many chemical properties that are not even defined within the method, such as electronic excited states. Since chemical bonding tenns are explicitly included in the force field, it is not possible without some sort of mathematical manipulation to examine reactions in which bonds are formed or broken. In order to work with extremely large and complicated systems, molecular mechanics software packages often have powerful and easy-to-use graphic interfaces. Because of this, mechanics is sometimes used because it is an easy, but not necessarily a good, way to describe a system. 

Another way to define the geometry of a molecule is as a set of Cartesian coordinates for each atom as shown in Figure 8.2. Graphic interface programs often generate Cartesian coordinates since this is the most convenient way to write those programs. 

Alchemy 2000 (we tested Version 2.05) is a graphic interface for running molecular mechanics and semiempirical calculations. Calculations can be done with the built-in Tripos force field or by calling the MM3 or MOPAC programs, which are included with the package. Alchemy is designed by Tripos and sold by SciVision. 

UniChem (we tested Version 4.1) is a graphic interface made for running calculations on remote machines. The UniChem GUI runs on the local workstation and submits the computations to be run on a remote machine. The server software comes with MNDO, DGauss, and CADPAC. It can also be used as a graphic interface for Gaussian and Q-Chem. A toolkit can be purchased separately, which allows users to create an interface to their own programs. 

At the time of this review, a new graphic user interface was under development. Jaguar can also be purchased as part of the Titan program, which combines Jaguar with the Spartan graphic interface. An orbital viewer for Jaguar is available from Serena Software. 

The HyperChem program from Hypercube Inc. and UniChem from Oxford Molecular can be used as graphic interfaces to Q-Chem. At the time we conducted our tests, it was not yet available on all the platforms listed as being supported. The current version is well designed for ground- and excited-state calculations on small or large organic molecules. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

The graphic interface is a multitasking environment that works well. The protein and carbohydrate builders are particularly convenient to use. The small-molecule builder has a selection of common organic functional groups as well as individual atoms for organics and common heteroatoms. There are a... 

GaussView (we used Version 2.08) is a graphic interface for use with the Gaussian ah initio program. It can be used to build molecules, set up the options in the input hie, 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 launches the calculation was not too dilficult to modify for use with a job-queueing system. 

Babel (we tested Version 1.6) is a utility for converting computational chemistry input hies from one format to another. It is able to interconvert about 50 different hie formats, including conversions between SMILES, Cartesian coordinate, and Z-matrix input. The algorithm that generates a Z-matrix from Cartesian coordinates is fairly simplistic, so the Z-matrix will correctly represent the geometry, but will not include symmetry, dummy atoms, and the like. Babel can be run with command line options or in a menu-driven mode. There have been some third-party graphic interfaces created for Babel. 

Submitting a structure to a calculation can be expensive in terms of human time and effort. HyperChem lets you build and display molecules easily. Since HyperChem contains a graphical interface, you can monitor the construction of molecules. 

Generating Cartesian coordinates by hand is only realistic for small molecules. If, however, the geometry is taken from outside sources, like for example an X-ray structure, Cartesian coordinates are often the natural choice. Similarly, a graphical interface produces a set of Cartesian coordinates for the underlying program, which carries out the actual calculation. 

As computer programs evolve they become easier to use. Modem programs often communicate with the user in terms of a graphical interface, and many methods have become essential black box procedures if you can draw the molecule, you can also do the calculation. This effectively means that you no longer have to be a highly trained theoretician to run even quite sophisticated calculations. 

MetabolExperF Rule-based Metabolite prediction software Predicts the most common metabolic pathways in animals, plants or through photodegradation. Results are presented in metabolic tree format. Graphical interface for editing and adding rules www.compudrug.com... 

SIMULINK Workstations, Mac and PC Based on MATLAB but with improved integration routines, model building blocks and graphical interface. 

Powerful mouse/menu controlled graphical interface creates system block diagrams, generates error-free simulation models, executes the simulation, and displays graphical results. 

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