IU MolViz Application Guide

The MolViz Application Guide pertains to topics, molecular modeling applications, and UNIX applications specific to the computing environment of the Molecular Visualization Facility of the Department of Chemistry at Indiana University.

If you have questions or suggestions regarding these notes, contact the MolViz Facility Staff.

Index

Application Guide

Activity Applications
Visualizing 3D molecular structures InsightII, Cerius2, MolMol, Molden, Molscript, PC-MODEL,  RasMol, Ribbons,  VMD, XMView, JaMM, Swiss-PdbViewer, Mercury, gOpenMol, MOLEKEL
Classical Mechanical Calculations PC-MODEL, Discover/InsightII
Quantum Mechanical Calculations Gaussian, MOPAC
Systematic Conformational Searches GMMX, YAMMP
Database Searches CSD
Calculation of Geometrical Properties Naccess, HBPlus, PROCHECK
Docking a small molecule and a large molecule AutoDock, DOCK, Dock/InsightII
Docking two large molecules not yet available
Calculating the Electrostatic Field of a Macromolecule DelPhi
Sequence Alignment and Model-Building ALSCRIPT, AMPS, STAMP
X-Ray Crystallography Applications O, CNS, XRayView
NMR Spectroscopy Applications CNS
Miscellaneous Applications Babel, GelTrak
 

Molecular Modeling Application List

 (IN ALPHABETICAL ORDER)
ALSCRIPT
Takes a multiple sequence alignment in AMPS block-file format and a set of formatting commands and produces a PostScript file that contains a sequence alignment figure suitable for publication.

AMPS
A suite of programs designed for multiple alignment of protein sequences and flexible pattern matching.
 
AutoDock
A Monte-Carlo computer simulation method for automated docking of flexible ligands to receptors. This non-graphical program has been augmented with scripts and notes for interfacing AutoDock results with InsightII.
 
BABEL
A program for translating one type of molecular structure file format to another file format.
 
Cambridge Structural Database
The CSD is the largest searchable database of experimentally determined crystal structures. This system includes graphical search, retrieval and data visualization software.
 
Cerius2
A comprehensive molecular modeling system. The suite of Cerius2 programs supported by the IU MolViz Facility is focused particularly for materials science modeling.
 
CNS
The Crystallography & NMR System for calculation of biomolecular structure models from crystallographic or NMR experimental results.
 
DelPhi
Calculates the electrostatic field generated by a molecule via the Poisson-Boltzmann Equation.

DOCK
Flexible ligand docking using a genetic algorithm.
 
Gaussian
A general-purpose Ab initio molecular orbital package. This application is designed to model a broad range of molecular systems under a variety of conditions, performing its computations starting from the basic laws of quantum mechanics.
 
Geltrak
A system for scanning one-dimensional gels, displaying lane profiles, and calculating areas under the peaks.
 
GMMX
GMMX is now built into PC-MODEL v7.0 and later versions. However, the original GMMX v1.0 program is retained here for backwards-compatibility.

gOpenMol
A molecular graphics toolbox for the display of molecules and their properties and the analysis of molecular structures and dynamics trajectories (originally as the graphics interface for the OpenMol set of programs).

HBPLUS
A hydrogen bond calculation program.
 
Insight II
A comprehensive molecular modeling system. The suite of Insight II programs supported by the IU MolViz Facility is focused particularly for bio-pharmaceutical modeling. Additional scripts are included for extra functionality.

JaMM
A locally written Java applet for examining molecular structures.

Mercury
A crystal structure visualizer developed by CCDC.
 
MOLDEN
A graphical pre- and post-processing package for displaying molecular and electronic structure from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac.

MOLEKEL
A molecular graphics program for displaying molecular and electronic structure data from electronic structure programs, such as GAUSSIAN 9x, ADF, and GAMESS-US.
 
MolMol
A molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
 
Molscript
A program for creating schematic or detailed molecular graphic images from molecular 3D coordinates (PDB files), usually, but not exclusively, protein structures.
 
Mopac
A general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. Additional notes and scripts are included for interfacing the input and output files of this non-graphical program with other programs.

Naccess
Calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface.
 
O
A Macromolecular Crystallography Package.
 
PC-MODEL
A complete molecular modeling package, especially for small molecules. One of the most user-friendly programs available. Draw structures, minimize structures, search for different conformations of structures, and dock two or more structures.
 
PROCHECK
Programs for assessing the overall geometrical quality of protein structures, for analyzing NMR ensembles, and for comparing related protein structures
 
RasMol
A molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
 
Ribbons
Interactively displays molecular models, creates publication quality images, and analyzes crystallographic results. Particularly intended for protein and nucleic acid models.

STAMP
Given a set of protein domains with a similar structure, one can use STAMP to produce a multiple alignment and associated superimposition based on a comparison of 3D structures.

Swiss-PdbViewer
A molecular graphics program for viewing and manipulating PDB files.

VMD
A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

XMView/CMView
XMView is a locally written Unix (& Linux) application which generate publication quality molecular graphics. CMView is the CAVE application that can be used in conjunction with XMView.
 
XRayView
This application uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals.
 
YAMMP
A package for molecular simulations, particularly for reduced representation models. There are several methods for Energy Minimization, Molecular Dynamics and Monte Carlo simulations.

xtel

UNIX Application Notes

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Last updated:  6/6/2002