This page is the main index for the MolArch⁺ installation and documentation site. MolArch⁺ is freely available for academic institutions only. Business companies or other commercial users may contact me via e-mail to obtain a license.

• MolArch+ - Prerequisites, Download, and Installation
• MolArch+ - Updates and Bug Fixes
• MolArch+ - Programs and Program Options
• MolArch+ - Parameter Files and Settings
• MolArch+ - File Types and Extensions
• MolArch+ - Quick Start and General Usage
• MolArch+ - Table of all Commands
• MolArch+ - Short Syntax of all Commands
• MolArch+ - Help File and Descriptions of all Commands
• MolArch+ - Examples for Graphics and Animations
• MolArch+ - Error Messages

You may also use the frames version of this documentation.

1. FITTING of Molecules:

   Least-squares 3D-fitting of molecules is performed via rigid-body translation and rotation.
   D. J. Heisterberg, QTRFIT - Rigid Body Rotation and Fitting Program, The Ohio Supercomputer Center, Columbus, Ohio 43212, 1991.

2. PIMM91 Force Field Program:

   (a) H. J. Lindner, M. Kroeker, PIMM91 - Closed Shell PI-SCF-LCAO-MO Molecular Mechanics Program, Technical University of Darmstadt, 1995.
   (b) A. E. Smith, H. J. Lindner, J. Comput.-Aided Mol. Des. 1991, 5, 235-262.
   http://www.oc.chemie.tu-darmstadt.de/lin/pimm.html

3. MOLCAD Molecular Modeling Program:

   (a) J. Brickmann, MOLCAD - MOLecular Computer Aided Design, Technical University of Darmstadt, 1992; J. Brickmann, J. Chim. Phys. 1992, 89, 1709-1721.
   (b) M. Waldherr-Teschner, T. Goetze, W. Heiden, M. Knoblauch, H. Vollhardt, and J. Brickmann, in: Advances in Scientific Visualization (Eds.: F. H. Post, A. J. S. Hin), Springer Verlag, Heidelberg, 1992, pp. 58-67.
   (c) J. Brickmann, T. Goetze, W. Heiden, G. Moeckel, S. Reiling, H. Vollhardt, and C.-D. Zachmann, Interactive Visualization of Molecular Scenarios with MOLCAD / SYBYL, in: Insight and Innovation in Data Visualization (Ed.: J. E. Bowie), Manning Publications Co., Greenwich, 1995.

4. MACROMODEL force-field program:

   Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.;Hendrickson, T.; Still, W. C. ,"MacroModel-An Integrated Software System for Modeling Organic and Bioorganic Molecules using Molecular Mechanics", J. Comput. Chem. 1990, 11, 440.

5. MM2/MM3 force-field:

   (a) Allinger, N. L. ,"Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1and V2 Torsional Terms", J. Am. Chem. Soc. 1977, 99, 8127.
   (b) Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. ,"Molecular Mechanics. The MM3 Force Field for Hydrocarbons", J. Am. Chem. Soc. 1989, 111, 8551.

6. ORTEP-III - Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations:

   Michael N. Burnett and Carroll K. Johnson, ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations, Oak Ridge National Laboratory Report ORNL-6895, 1996.
   http://www.ornl.gov/ortep/

7. HIRSHFELD-SURFACES - A New Tool for Visualizing and Exploring Molecular Crystals:

   Joshua J. McKinnon, Anthony S. Mitchell, Mark A. Spackman, Chemistry - A European Journal 1998, 4, 2136-2141.

8. SHELX-97 - X-Ray Structure Solution and Refinement:

   http://shelx.uni-ac.gwdg.de/ and http://shelx.uni-ac.gwdg.de/SHELX/

9. VRML in Chemistry:

   (a) H. Vollhardt, C. Henn, M. Teschner, and J. Brickmann, Virtual reality modeling language in chemistry, J. Mol. Graphics 1995, 13, 368.
   (b) H. Vollhardt, G. Moeckel, C. Henn, M. Teschner, and J. Brickmann, "VRML in Chemistry".

10. POVRAY - Persistence of Vision Ray Tracer:

    http://www.povray.org

11. GNUPLOT - Scientific Plotting:

    http://www.gnuplot.info/

12. XFARBE - 2D-Contour Plot Program:

    Preusser, A., Algorithm 671 - FARB-E-2D: Fill Area with Bicubics on Rectangles - A Contour Plot Program. ACM Transactions on Mathematical Software, Vol. 15, No. 1, March 1989, p. 79-89.
    http://www.fhi-berlin.mpg.de/~grz/pub/xfarbe.html

13. MolArch⁺ and MolView⁺ Molecular Modeling Programs:

    S. Immel, MolArch⁺ - MOLecular ARCHitecture+ modeling program V7.35 09.MAY.2003, Technical University of Darmstadt.

14. MolCont⁺ - 3D-Contouring and Triangulation Program:

    S. Immel, MolCont⁺ - 2D- and 3D-Contouring Program for Orthogonal and Polar Coordinate Data Sets V7.35 09.MAY.2003, Technical University of Darmstadt.