5. Features

• supported hardware and operating systems
  • Silicon Graphics (IRIX 4.X, 5.X)
  • Sun SPARC (SunOS 4.X, Solaris 2.X)
  • IBM RS6000 (AIX)
  • Digital ALPHA (OSF/1)
  • Linux
  • PCs with Intel Pentium (Windows NT/95)
• 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)
  • 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/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
• 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
  • plates for rings (e. g. for DNA)
  • 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
• 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, ...)
  • end styles: sharp, soft, arrow
  • splines with variable radius (e. g. for mobility)
  • change width, thickness, size of arrow, ...
  • 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)
  • VRML
• 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

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MOLMOL Manual - 7 Oct 1997

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