Software

Multi-Purpose Modeling/Graphics

Molecular graphics is an integral part of SYBYL's graphical user interface. Molecular structures can be represented in a variety of ways in SYBYL, including bonds only and atom drawing styles, and mixtures thereof. Surfaces can be drawn for a variety of properties. Surface drawing styles include dot, solid (transparent or opaque), and wire-mesh. Ribbon representations specialized for biopolymers are also available. Up to four graphical molecular structure representations can be independently transformed in space. Bond rotations can also be performed graphically. A number of visualization aides are available.

Interactive Visualization

Several interactive viewing programs are available for Mac's, PC's and Unix platforms, including:

  1. GEMM.
  2. Kinemage.
  3. MacImdad.
  4. NanoVision.
  5. RasMol (described via electronic documentation).
  6. XMol (described via electronic documentation).

Some of these programs can be used in conjunction with "Molecules R US" and "Small Molecules R US" to view molecular structures obtained from network-based structure databases.

Fancy Output for Printed Documents

Molecular graphics programs tend to be specialized at either PostScript or bitmap output (described and compared elsewhere). Bitmap output can be created directly by some molecular graphics programs or from any screen image via an image capture tool. Bitmap files can be processed into PostScript via a format conversion utility.

MolScript and Setor are programs specialized for the direct creation of PostScript output (mostly geared to protein structures). MolScript is operated via a command script rather than a graphical interface, however the interactive viewer, RasMol, can be used as a graphical front end for MolScript, and in particular, can provide the sequence positions of protein secondary structure elements required by MolScript.

Raster3D is a collection of programs specialized for the direct creation of bitmap output. The capabilities of Raster3D to draw protein ribbon structures can be greatly enhanced using MolScript as a pre-processor. Furthermore, Raster3D can be used to create high resolution printed output.

SYBYL produces reasonable quality color shaded space-filling and ball-stick drawings in PostScript.