Molmol

From MarcsHomepage

Introduction

Molmol has been written at the ETH Zürich by Reto Koradi, a member of the Wuethrich group with support from Bruker Biospin. Molmol was originally intended for use with UNIX-based workstations running X11 and OpenGL. Reto Koradi ported the version 2.4-package to Windows.

User Interface

Molmol1.jpg

The user-interface of Molmol is based on the UNIX-version, which might be a bit puzzling for people who are only accustomed to Microsoft Windows-environments.
Nevertheless Molmol is the most powerful of all programs mentioned in this review, apart from Pymol and VMD maybe. It has a huge number of features for display, manipulation, mutation and editing of molecular data-files. The result of this is a quite complex user-interface with a somewhat cryptic language. But if you get used to the concept of Molmol and especially it´s command-language, you have a very powerful and efficient tool. One big advantage is that you can control the whole program with macros and shell-scripts. Even the menu´s and pushbuttons are fully customizable (most of the pushbuttons are macros in fact). You can record and save your own macros, making it easy to solve complex tasks by pressing one or two keys after you have solved them once.

Features

Molmol features the following things (taken from the Molmol-homepage)

  • 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 browser)
    • 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 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
    • 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)
    • dotted 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

There is a extensive help system (although I would prefer a real Windows-help or man-pages) and online-manual both in DVI, EPS, and HTML-format. One can save excellent POVRay-Source-Files as well as very good screenshot-images for publications (see the Output-page).

The program also has some drawbacks of course: It has problems with molecules which are not protein- or DNA-based. Sometimes you can solve this by calculating the bonds between the atoms of the unknown molecule, and you can save this information, but this part has been solved more properly in the other software packages.