XCrySDen-a new program for displaying crystalline structures and electron densities

Journal of Molecular Graphics and Modelling

Volumn 17, Issue 3-4, 1999, Pages 176-179

  Kokalj, Anton ^a  

^a JO EF STEFAN INSTITUTE   (Slovenia)

Author keywords

Crystalline graphics; Electronic density; Isosurfaces; Modelling; Molecular graphics

Indexed keywords

ALGORITHM; ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; COMPUTER; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DENSITY; ELECTRON; INTERFEROMETRY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; OXYGEN; PLATINUM; SOFTWARE;

EID: 0033497492     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(99)00028-5     Document Type: Article

References (25)

1. Sayle, R. Rasmol v2.5 - A Molecular Visualisation Program. Glaxo Research and Development Greenford, Middlesex, UK; Sayle, R.A., and Milner-White, S.C. RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 1995, 20, 374-376.
2. Minnesota Supercomputer Center. Xmol User Guide, version 1.3.1. Minnesota Supercomputer Center, Inc., Minneapolis, Minnesota, 1993.
3. Schaftenaar, G. MOLDEN: A Portable Electron Density Program. Quantum Chemical Program Exchange QCPE619; MOLDEN: A pre and post-processing program of molecular and electronic structure. http://www.caos.kun.nl/~schaft/molden/molden.html.
4. Koradi R., Billeter M., Wüthrich K. MOLMOL A program for display and analysis of macromolecular structures . J. Mol. Graphics. 14:1996;51-55.
5. Johnson, E.L., and Reichard, K. X Window Applications Programming, MIS, Inc., a subsidiary of Henry Holt and Company, New York, 1992.
6. GNU Library General Public License, version 2. Free Software Foundation, Boston, 1991.
7. Silicon Graphics, Inc. The OpenGL Programming Guide. Addison-Wesley, Reading, Massachusetts, 1993.
8. Paul, B. Mesa - The Free OpenGL Work-Alike Library. http://www.mesa3d.org/. 1999.
9. Zhao, T.C., and Overmars, M. XForms - Forms Library: A Graphical User Interface Toolkit for X. http://bragg.phys.uwm.edu/xforms. 1999.
10. Ascher, D., and Lutz, M. Learning Python. O'Reilly & Associates, Beijing, 1999; Python - interpreted, interactive, object-oriented, extensible programming language. http://www.dstc.edu.au/python/. 1997.
11. Amundson, S.T. The GIMP Toolkit. http://www.gtk.org/. 1999.
12. Ousterhout, J.K. Tcl and the Tk Toolkit. Professional Computing Series. Addison-Wesley, Reading, Massachusetts, 1994; Welch, B.B. Practical Programming in Tcl and TK. Prentice Hall PTR, Englewood Cliffs, New Jersey, 1995; some information about Tcl/Tk can be browsed from http://www.tclconsortium.org/, http://www.elf.org/, and http://www.tcltk.com/.
13. Linux is a free Unix-type operating system originally created by Linus Torvalds with the assistance of developers around the world. Linux is an independent POSIX implementation and includes true multitasking, virtual memory, shared libraries, demand loading, proper memory management, TCP/IP networking, and other features consistent with Unix-type systems. Developed under the GNU General Public License,6 the source code for Linux is freely available to everyone. The web site of Linux can be found at http://www.linux.org/.
14. Awk was written by: Aho, V.A., Weinberger, P.J., and Kernighan, B.W. at AT&T Bell Laboratories, 1997; Robbins, A.D. AWK Language Programming, A User's Guide for GNU AWK, 1996.
15. Network Computing Services, Inc. XYZ Format. http://www.msc.edu/msc/docs/xmol/XMol.html. 1995.
16. Brookhaven Protein Data Bank. PDB Format. http://www.pdb.bnl.gov/. 1999.
17. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: Chemistry at Harvard Macromolecular Mechanics. J. Comput. Chem. 4:1983;187.
18. J.L. Finney. J. Comput. Phys. 1979, 32, 137.
19. Jarvis, R.A. On the identification of the convex hull of a finite set of points in the plane. Inf. Proc. Lett. 1973, 2, 18-21; Cormen, T.H., et al. Introduction to Algorithms. MIT Press, Cambridge 1990.
20. Knuth, D.E. Sorting and Searching. The Art of Computer Programming. Reading, MA: Addison-Wesley, 1973, vol. 3. Sedgewick, R., Algorithms. 2nd ed., Reading, MA: Addison-Wesley 1988, Chapter 11. Press, W.H., Teukolsky, S.A., Vetterling, W.T., Flannery, B.P. Numerical Recepies in Fortran 77: The Art of Scientific Computing. 2nd ed., Cambridge University Press, 1992, Chapter 8.
21. Knuth, D.E. Sorting and Searching. The Art of Computer Programming. Reading, MA: Addison-Wesley, 1973, vol. 3. Sedgewick, R., Algorithms. 2nd ed., Reading, MA: Addison-Wesley 1988, Chapter 11. Press, W.H., Teukolsky, S.A., Vetterling, W.T., Flannery, B.P. Numerical Recepies in Fortran 77: The Art of Scientific Computing. 2nd ed., Cambridge University Press, 1992, Chapter 8.
22. Knuth, D.E. Sorting and Searching. The Art of Computer Programming. Reading, MA: Addison-Wesley, 1973, vol. 3. Sedgewick, R., Algorithms. 2nd ed., Reading, MA: Addison-Wesley 1988, Chapter 11. Press, W.H., Teukolsky, S.A., Vetterling, W.T., Flannery, B.P. Numerical Recepies in Fortran 77: The Art of Scientific Computing. 2nd ed., Cambridge University Press, 1992, Chapter 8.
23. Williams, T., and Kelley, C. Gnuplot-An Interactive Plotting Program. http://www.cs.dartmouth.edu/gnuplot/gnuplot.html. 1995.
24. Lorensen W., Cline H. Comput. Graphics. 21:1987;163.
25. Bourke, P. Modelling. http://www.swin.edu.au/astronomy/pbourke/modelling/. 1999.