Section 25.1.9. Structure presentation

GRASP (Nicholls et al., 1991) is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. Its particular strength compared to other such programs is its facility for surfaces and electrostatics. The program contains extremely rapid algorithms for the construction of rendered molecular surfaces and for solving the Poisson–Boltzmann equation. GRASP's surface can be molecular or accessible and can be colour-coded by electrostatic potential derived from its internal Poisson–Boltzmann solver or external programs such as DelPhi. This representation has become a standard tool in assessing electrostatic character of large, typically protein, molecules. Surfaces can also be coloured by other properties, such as any of those of the underlying atoms (e.g. hydrophobicity) or by its own intrinsic properties, such as local curvature. The program also contains several other unique data-representation forms in addition to standard ones such as ball-and-stick for atoms and bonds, and backbone splines, or `worms', to indicate secondary structure. See Chapter 22.3 for more details.

Location: http://honiglab.cpmc.columbia.edu/grasp/ . Operating system: IRIX. Type: binary. Distribution: commercial.

The LIGPLOT program (Wallace et al., 1995) automatically generates schematic diagrams of protein–ligand interactions for a given PDB file. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts.

Location: http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html . Operating systems: UNIX, IRIX and LINUX. Type: source code. Language: C. Distribution: free academic.

MOLSCRIPT (Kraulis, 1991) is a program for creating schematic or detailed molecular-graphics images in the form of PostScript plot files from molecular 3D coordinates, usually, but not exclusively, of protein structures. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Colour, greyscale, shading and depth cueing can be applied to the various graphical objects. See Section 25.2.7 for a detailed description.

Location: http://www.avatar.se/molscript/ . Operating system: UNIX. Type: source code and binary. Language: C. Distribution: free academic.

An enhanced variant of MOLSCRIPT, called BOBSCRIPT, has been developed by Robert Esnouf (http://orval.rega.kuleuven.ac.be/∼robert/Bobscript/ ). In addition to the functions provided by MOLSCRIPT, BOBSCRIPT can generate an input file automatically and allows for the display of electron density.

NUCPLOT (Luscombe et al., 1997) is a program which generates schematic diagrams of protein–nucleic acid interactions. The program automatically identifies these interactions from the 3D atomic coordinates of the complex from a PDB file and generates a plot that shows them in a clear and simple manner.

Location: http://www.biochem.ucl.ac.uk/bsm/nucplot.html . Operating systems: UNIX, IRIX, LINUX and Windows. Type: source code. Language: C. Distribution: free academic.

The Oak Ridge Thermal Ellipsoid Plot (ORTEP, version III) program (Burnett & Johnson, 1996) is a computer program for drawing crystal-structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are generated with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature-factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations that aid in the visualization of complex arrangements of atoms and their correlated thermal-motion patterns.

Location: http://www.ornl.gov/ortep/ortep.html . Operating systems: UNIX, LINUX, DOS, MacOS and Windows. Type: source code and binary. Language: Fortran77. Distribution: free.

RasMol is 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 high-quality images for publication. It is easy to use and produces beautiful space-filling three-dimensional colour images. RasMol reads in molecular coordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory rendering (via the XInput and MIT-SHM extensions) if available.

Location: http://www.umass.edu/microbio/rasmol/ . Operating systems: UNIX, VAX/VMS, Windows and MacOS. Type: source code. Distribution: free.

Raster 3D (Bacon & Anderson, 1988; Merritt & Murphy, 1994; Merritt & Bacon, 1997) is a set of tools for generating high-quality raster images of proteins or other molecules. The core program renders spheres, triangles and cylinders with special highlighting, Phong shading and shadowing. It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball-and-stick etc. Raster3D can also be used to render pictures composed in Per Kraulis' program MOLSCRIPT (Section 25.1.9.3) in glorious 3D with highlights, shadowing etc. Output is pixel image files with 24 bits of colour information per pixel.

Location: http://www.bmsc.washington.edu/raster3d/raster3d.html . Operating systems: DEC, SGI, ESV, SUN, IBM, HP and LINUX. Type: source code and binary. Distribution: free.

Ribbons software (Carson & Bugg, 1986; Carson, 1997) interactively displays molecular models, analyses crystallographic results and creates publication-quality images. Space-filling and ball-and-stick representations, dot and triangular surfaces, electron-density-map contours, and text are also supported. Input atomic coordinates are in Protein Data Bank (PDB) format. Output may be produced in the Inventor/VRML format.

Location: http://sgce.cbse.uab.edu/ribbons/ . Operating systems: UNIX, LINUX and PC. Type: source code and binary. Distribution: commercial.

SETOR (S. V. Evans, 1993) is designed to render high-quality raster images of macromolecules that can undergo rotation and translation interactively. SETOR can render standard all-atom and backbone models of proteins or nucleic acids, but focuses on displaying protein molecules by highlighting elements of secondary structure. The program has a very friendly user interface that minimizes the number of input files by allowing the user to interactively edit parameters such as colours, lighting coefficients and descriptions of secondary structure via mouse-activated dialogue boxes. The choice of polymer-chain representation can be varied from standard vector models and van der Waals models, to a beta-spline fit of polymer backbones that yields a smooth ribbon, and to strict Cardinal splines that interpolate the smoothest curve possible that will precisely follow the polymer chain. The program provides a photograph mode, save/restore facilities, and efficient generation of symmetry-related molecules and packing diagrams. Additionally, SETOR is designed to accept commands and model coordinates from standard output. Ancillary programs provide a method to edit interactively hardcopy plots of all vectors and many solid models generated by SETOR, and to produce standard HPGL or PostScript files.

Location: http://www.csb.yale.edu/userguides/graphics/setor/setor_descrip.html . Operating system: SGI. Type: binary. Distribution: commercial.

VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies etc. It may be used to view more general molecules, as VMD can read standard PDB files and display the structure contained in them. VMD provides a wide variety of methods for rendering and colouring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyse the trajectory of a molecular-dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Location: http://www.ks.uiuc.edu/Research/vmd/allversions . Operating systems: SGI, SUN, DEC Alpha, IBM AIX, HP-UX and LINUX. Type: binary. Distribution: free.