Mol2Mol 5.6 summary of features
Conversion of file formats:
- During the conversion, the bond and atom types are automatically calculated, if necessary (and possible).
- Perception of aromaticity, if necessary (in 5-6 membered planar rings). Option to use s/d bonds or aromatic ones.
- Automatic checking of supported atom and bond types (not all of the formats support for example lone-pairs or aromatic or coordinative bonds etc.)
- Display in simple vector, thick vector or ball-and-stick modes.
- Showing of atom aliases, adding implicite hydrogens in 2D files.
- Red-and-green or cross-eyed stereo modes.
- Rotation, translation and zooming with the mouse or by buttons.
- Screen and world coordinates are handled separately.
- Automatic display of the coordinates, atom type, atom label, atom charges, chain/residue info of the selected atom.
- Toggling the display of coordinate system axes.
- Copy the image to the clipboard in bmp format.
- Coloring according to models/chains/residues/alternative locations and helix/sheet/turn info.
- Selection according to models/chains/residues.
- Display of the selections only.
- Display of the vicinity of a selected atom (within 4 or 6 bonds, given distance) only.
Manipulation of the molecule:
- Removing of lone-pairs, dummy atoms, water molecules, special bonds, formal charges.
- Adding of all hydrogens automatically, in the case of PDB files in pH dependent mode too.
- Automatic assigning and creating of H-bonds.
- Manual editing of atom types from the graphics window.
- Direct call of your favorite text editor with the last input or output file to manually edit problematic files.
- Adding of hydrogens in manual mode one-by-one according to a selected geometry.
- Automatic assigning of bond types.
- Manual adding, removing or changing of bonds and their types (1-2-3, amide, aromatic, coordinative, ionic, H- or weak, unknown, dummy types are supported, depends on the concrete file type in use).
- Centering of the molecule at the centre of mass, geometric centre or selected atom.
- Advanced rotation and translation methods (align bond with axes, turn atoms into plane etc).
- Conversion to enantiomer.
- Proteins/DNA: conversion to backbone or CA-atom-only "molecules".
- Renumbering of atoms by several options.
Different utilities included:
- Calculation of bond lengths, angles, dihedrals in different manners.
- One-run batch calculation of several similar data of several files or models in multiple files.
- Find all dihedrals of an atom.
- Dihedral angle of least square (mean) planes.
- Distance of selected atom from least-square (mean) plane.
- Pyramidality of atoms (4 different indices).
- Calculation of ring puckerings (in 5-9 membered rings).
- Calculation of Gasteiger-Marsili charges; changing of formal charges.
- Calculation of sterimol parameters, bounding box and dipol moment.
- Superimpoising and rms comparison of two molecules, using all atoms or only selected ones, optionally with different weight factors. Multiple mode supported.
Utilities concerning peptides/DNA:
- Displaying the backbone only.
- Conversion to backbone or CA-atom-only "molecules"
- Calculation of phi-psi-omega values and show Ramachandran plot.
- Removing of all but one alternative locations.
- Zoom in and step along any part of the structure, in combination with:
- Checking of geometry and mistakes in peptide backbones (very useful).
Utilities concerning NMR:
- Calculation of distances between selected hydrogens and/or Me-centroids.
- Showing hydrogens within a given distance range from other hydrogens or Me-centroids.
- Adding of CH2 or CH3 centroids as dummy atoms.
Supported file formats (Read and/or Write):
|MDL mol (vers. 1-2 or 3), sdf|
|MDL rxn, rdf|
|CSSR, Desktop MM|
|Brookhaven PDB, PDBQ and Chime versions|
|Z-matrix several free formats, MOPAC and user defined format|
|Gamess input and output files|
|Q-Chem input file|
|Turbomol input and output file|
|Gaussian input and output|
|Cartesian several free formats and user defined format|
|X-ray fractional free format: CIF, multiple CIF, SHELX, FDAT, MODEL, CSSR