# Features

- hardware platforms and operating systems supported by official distribution
  - Silicon Graphics (IRIX 6.5)
  - PCs with Intel Pentium (Linux)
  - PCs with Intel Pentium (Windows NT/95/98)
- other hardware platforms and operating systems that the source code has been successfully compiled on
  - Silicon Graphics (IRIX 4.X, 5.X, 6.2)
  - Sun SPARC (SunOS 4.X, Solaris 2.X)
  - IBM RS6000 (AIX)
  - Digital ALPHA (OSF/1)
  - various Linux platforms
- display systems
  - GL (Silicon Graphics), including stereo display
  - OpenGL, including stereo display
  - XGL (Sun)
  - X11
  - TTY (no graphics)
- user interface
  - command line with automatic command completion and history
  - pulldown menus (created from ASCII file)
  - popup menu (created from ASCII file)
  - buttons (created from ASCII file)
  - dialog boxes
  - slider box
  - online help (optionally in web broser)
  - Tip of the Day
  - log window
  - macro recorder
  - user-defined commands
  - undo (multiple level)
- interactive manipulations (selected subset of molecules)
  - rotations (virtual trackball)
  - translations
  - zoom
- data input/output
  - read residue library
  - write entries for residue library
  - read/write PDB file
  - read list of PDB files
  - read/write DIANA angle file
  - read list of DIANA angle files
  - read/write DG file
  - read list of DG files
  - read SYBYL Mol2 files
  - read XYZ files
  - read/write sequence
  - read/write binary file (with full graphics information)
  - replace coordinates with new ones from PDB file
  - replace coordinates with new ones from list of PDB files
  - replace coordinates with new ones from DG file
  - replace coordinates with new ones from list of DG files
  - read/write file with distance constraints
  - read file with angle constraints
  - read file with chemical shifts
  - save/load orientation
- create entries in residue library (from DG and PDP format)
- structure manipulation
  - create new molecule
  - change molecule name
  - add residue at start or end
  - change residue (mutation)
  - remove residue
  - add/remove atoms
  - add pseudo atom
  - flip ring/methyl atoms for better superposition
  - add bond
  - generate bonds between atoms with close distance
  - remove bonds
  - add/remove angles
  - add/remove angle constraints
  - calculate mean structure
- definition of distances (constraints, H-bonds)
- setting of dihedral angles (construction of helices,...)
- interactive rotation about single bonds
- calculation of superpositions and principal axes
- selection
  - with general expressions
  - interactively
  - list selected items
- display possibilities
  - select light position
  - intensity of ambient light
  - select projection (orthogonal or perspective)
  - anti aliasing
  - depth cueing (set fog density)
  - normal bonds or bonds to pseudo atoms
  - bonds: invisible, lines, half lines, cylinders, half cylinders, cones, half cones
  - atoms: invisible, spheres or tetrahedrons
  - distances: invisible, line, cylinder, cone (also dashed)
  - atom labels
  - circles for B-factors
  - constraints
  - violations
  - electron density maps (from O)
  - plates for rings (e. g. for DNA)
  - principal axes
  - dottet or shaded, colored molecule surfaces (VdW, solvent accessible, contact), optionally trimmed
  - isosurfaces of electrostatic potential
  - MD trajectories (with lines or cylinders)
  - MD runs (animation)
  - automatic rotation
  - stereo (left, right, side-by-side, cross-eye)
- labels and annotation
  - placement in 2D and 3D (stereo)
  - super-/subscript
  - symbols (greek letters)
  - edit
  - interactive move/resize
  - draw lines, rectangles and circles
- display attributes
  - color
  - line width
  - line style
  - reflection coefficients (ambient, diffuse, specular, shininess)
  - reflection, texture/image, bumpiness (for ray tracing)
  - shading (none, flat, Gouraud, Phong, dots, lines)
  - radius (cylinders, spheres and splines)
  - list current attributes, create macro
  - change default attributes
- schematic display
  - read secondary structure information from PDB file
  - calculate secondary structure (Kabsch/Sander algorithm)
  - ribbons (for helices, sheets), splines (turns, coil)
  - split/merge elements
  - change start and end position of elements
  - various profiles (elliptical, rectangular, \ldots)
  - end styles: sharp, soft, arrow
  - splines with variable radius (e. g. for mobility)
  - change width, thickness, size of arrow, \ldots
  - one, two or variable colors
  - cylinders (can be moved and resized), optionally with arrow head
  - dipolar moments as arrows
  - surfaces for beta-sheets
  - solids (sphere, ellipsoid, cylinder, cone, box)
- plotting
  - PostScript (portrait/landscape, also with stereo, shading, depth cueing and hidden surface elimination)
  - FrameMaker (MIF), for FrameMaker 3 (only 8 colors) and FrameMaker 4 (many colors)
  - Enhanced MetaFile (Windows)
  - image formats: TIFF, JPEG, PNG, BMP
  - POV-Ray (ray tracing)
  - RenderMan Interface Bytestream
  - VRML 1.0
  - VRML 2.0 (VRML97)
- calculations
  - global RMSDs with average, standard deviation, minimum and maximum
  - global displacements
  - local RMSDs
  - local displacements
  - RMSD calculations for groups of structures
  - calculate best matching structure parts
  - reduce number of structures (calculate clusters of similar structures)
  - solvent accessible surface of residues
  - electrostatic potential
  - ring current and bond polarization shifts
  - missing atom coordinates (protons, pseudo atoms)
  - angular order parameters
  - angles between helix axes
  - relative lengths of principal axes
  - angles of bonds relative to principal axes
  - find/generate bonds between close atoms
  - find/generate H-bonds
  - find Van der Waals violations
  - find short distances between atoms, generate peak list
  - check distance constraints
  - check angle constraints
  - all functions listed above also for groups (complexes)
  - interactive measurement of bond lengths, bond angles and dihedrals
- figures
  - Ramachandran plots (in color, with allowed regions and angle constraints)
  - angle distribution plots with dots inside bars (in color)
  - angle distribution plots in circles (for MD)
  - distance vs. structure number (for MD)
  - contact maps
  - maps of distance constraints
- history
- command macros

Last modified: Mon Jan 20 19:44:59 CST 2003