Mol2Mol 5.6 summary of features
For details open the Mol2Mol in a nutshell pages.
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
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, shows stereo bonds.
- Showing of atom aliases, adding implicite hydrogens in 2D files.
- Red-and-green/blue 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 a selected atom from a 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.
Special remarks concerning a few file types:
- Most of the file formats are recognized automatically.
- MDL mol and sd:
Changes automatically between simple molfile and multiple (sd) file.
Four subformats are supported: the "classical" one, the 1996 revised format, the PDBQ format (containing partial charges) and Chime/Rasmol format (with double and triple bond info and partial charges).
Selected input of models and/or chains.
Input subformats supported: general free format, stand alone Gaussian Z-matrix with/without symbolics, MOPAC, Q-Chem.
Automatic remove of possible dummy atoms.
Generation of new Z-matrix by two algorythms: star method or chain method.
Output subformats: free format with several formatting options, MOPAC, Gamess, Q-Chem, Gaussian with symbolics.
Input: free format with automatic recognition (with/without line numbering, atom symbols/numbers before/after the coordinates, presence/absence of charges).
Output: free format with a number options (2D/3D, atom symbols/numbers before/after the coordinates, labelled atoms yes/no).
Angstrom, nanometer or polar coordinates
- Input of Gamess and Gaussian 98 and 03 output files:
the current textual output of these files are used to grab the coordinates. These may be different in old or future versions.
Models: Spacefil (spheres or blobs), thick vector, ball&stick, different type can be applied for the selected part of the molecule.
Bonds: with/without bond types (1-2-3 and special). Bond coloring: uniform or atom colors; gradient fill coloring is supported.
Coloring according to models/chain/residues or helix/sheet/turn info; gradient coloring by atom charges or other computed properties.
Backbone of peptides/DNA as splines.
Transparently shaded rings.
Delocalized circles in planar rings.
Automatic insertion of headers and footers into the pov scene description file, automatic calculation of base planes.
Ample use of #declare statements to easy editing and customizing later...and several smaller options.
Adding of hydrogens as real atoms or as HFIX lines; REMing and un-REMing of input HFIX lines.\
Editing of Q atoms: selective remove, rename, adding of connections, checking of distances from neighbours.