Wire frame display with atom-colour-coded half bonds.
Wire frame display with colour-coded molecular entities.
Red-green stereo wire frame display.
DISPLAY MODES FOR STRUCTURES (with lighting model)
CPK mode display. Atom-coded ball and wire frame display.
Cylindrical bonds colour coded for bond-order.
Cylindrical bonds with atom-colour-coded half-bonds. ).
SINGLE, DUAL, QUADRUPLE DISPLAY MODES
Display of a single structure, or of two or four structures
simultaneously. (Structures labelled A, B, C, and D)
MANIPULATION OF STRUCTURES
Rotation on X, Y, Z, screen axes
Increase/decrease of size of structure
Display/hide hydrogen atoms
OPERATIONS ON STRUCTURES
Centre display on specified atom
Centre display on centre of molecule
Move structure on x, y, or z axes of screen
Calculate non-bonded distances
Calculate bond angles
Calculate torsion angles
Calculate the angle between two planes, each plane being defines by
three sets of atom coordinates
Identify chiral centres and characterize as having R or S configuration
(C, N, and S atoms)
Characterize double bonds as having E or Z configuration
Invert structure about centroid
Reflect structure in XY, XZ, or YZ plane
Rotation of chain segment
Loci of atoms on rotation of chain segment
View down specified bond
Remove hydrogens from structure
Manually renumber the structure
Renumber structure using Morgan's algorithm
Find molecular formula, molecular weight, and masses of molecular ions
in mass spectrum.
Investigate the likely presence of hydrogen bonds
INVESTIGATION OF ENERGETICS OF BOND ROTATION
Energy profile for rotation of a fragment about one bond
Energy profile for rotation of a fragment about two bonds
Energy map for rotation of a fragment about two bonds
STRUCTURE FITTING AND COMPARISON
Fitting of any of the structures, A, B, C, D on to one of the others by
Three point fit
Least-squares fit of between 3 and 25 atom pairs
Least-squares fit with fragment rotation
It is possible to align two molecules, without reference to their
molecular structures, using as matching parameters, either the overall
shape of the molecules, or the potentials on surfaces surrounding the
molecules. (Method of Icosahedral Matching).
STRUCTURE EXCHANGE AND COPYING
Any one of the structures A, B, C, D may be copied into any of the
Any pair of structures chosen from A, B, C, and D may be exchanged
The pairs of structures A and B, or C and D, may be merged to give a
Full control of the process is achieved interactively on the screen,
allowing the second (mobile) structure to be positioned and oriented
relative to the first structure.
Indication is given to the operator of unacceptable non-bonded
Desirable non-bonded interactions can be displayed
Merging can be controlled so that a specified distance between atoms in
the two structures may be met.
Merged structures can optionally retain record of components
New structures can be modelled interactively starting from a
comprehensive library of fragments.
A previously made structure can be recalled and further modified.
The current structure can be stored away at any time.
Building takes place by adding to the current (base) structure a chosen
Two basic operations are provided:-
Form one bond between base structure and fragment
Form two bonds between base structure and fragment (i.e. make a ring)
Other facilities provided include:-
Invert base or fragment structure
Reflect base or fragment structure in XY, XZ, or YZ planes
Alter atom(s) in base structure
Delete atom(s) in base or fragment structure
Alter bond(s) in base structure
Delete bond(s) in base structure
Form bond(s) in base structure
Remove all hydrogens from base structure
Add hydrogens to base structure
Create dummy atoms in base structure
Copy base structure to fragment area
Exchange base structure and fragment
Renumber base structure
Rotate a mobile side chain in either base structure or fragment
The option of undoing the last operation is provided, so allowing
mistakes to be rectified.
At any stage in the building process, the current base structure can be
optimised using the molecular mechanics program ICMECH. This process
usually takes only a few seconds. The optimised structure is then
displayed, and further extension can be carried out.
INPUT USING SMILES STRINGS
Structures may be entered in the form of linear SMILES strings. The
molecular mechanics module ICMECH is used to produce an optimised 3D
structure which in most cases is the minimum energy structure.
In cases where the minimum energy structure is not produced, a series
of structures may be produced for individual examination.
Stereochemical information may be included in the SMILES strings
SKETCHING OF STRUCTURES
A sketchpad is provided to allow input of essentially 2D structures.
These may be stored as such (for inclusion in a 2D database) or
converted to 3D structures which are optimised using ICMECH.
Correct 3D convertion is achieved using "hints" for the third
Define a central common scaffold structure with up to four attachment
Define up to four series of attachable groups (ligands)
Start a combinatorial process to generate up to 10,000 structures
optimized using molecular mechanics (ICMECH).
STORAGE OF STRUCTURES
INTERCHEM has a well defined format for storage of structures, that is
used to store both small and large molecules, including the fragments
in the fragment catalogue.
INTERFACES TO OTHER PROGRAMS
Structures produced by INTERCHEM can be stored in files with formats
suitable for submission to other programs:-
The semi-empirical molecular orbital program MOPAC
The structural data output from MOPAC can be read back into INTERCHEM.
The ab initio program GAMESS-UK.
SPECIAL FACILITIES FOR EXAMINING PROTEIN AND NUCLEIC ACID STRUCTURES
Besides the normal display methods there are special functions
Colour coded wire frame display to show amino-acid or nucleotide
Display to highlight structural features of proteins and nucleic acids.
Colour coded wire frame display to differentiate protein chains.
Display of protein structures as ribbons (also in red-green stereo).
Protein structures may be edited to select individual chains or
Protein Analysis Module
Polarity and Genetic Uniquness plots
Inter-residue distance plots
Contact with Protein Data Bank (or a mirror site) can be made from
within the program. Structure files can be downloaded by ftp, and
tranformed into INTERCHEM format by using PROTEINS-PC
SPECIAL FEATURES FOR THE EXAMINATION OF CRYSTAL STRUCTURES
Data files from the Cambridge Crystallographic Data Base may be loaded
into the system.
Data in CIF format is accepted.
The symmetry operations of the appropriate space group may be applied
to give the structure of a single unit cell, or alternatively a nest of
cells may be formed.
Provision is made for displaying the crystal axes, crystal (Miller)
planes, and an arbitrary defined axis.
This axis could be (for example) an experimentally determined principal
A comprehensive editing facility is present which allows the cleavage
planes of the crystal to be exposed. Using this and the merge facility
(see above) layering of one material on a substrate may be modelled.
FACILITY FOR DISPLAYING SERIES OF STRUCTURES
A set of structures can be displayed in one window of the dual display
at a rate of (say) one every three seconds.
Visual comparison with a (fixed) target structure in the second window
allows rapid selection of the best matches to the target.
Sets of conformers generated from a SMILES string (see above) can also
be viewed in this manner.
Hardware A personal computer running one of the
following versions of Microsoft Windows (32 or 64 bit).
If you want to recompile the the program from source code you must have
the Salford Fortran-95 compiler and Clearwin+ utility.
1280 x 1024 (preferable)
1400 x 1050
1680 x 1050
1920 x 1200
1024 x 768 are supported
Dual screen systems are also supported
Runs on portable computers meeting these resolution specifications
Stereo Viewing is supported if the necessary hardware is
A 120 page manual accompanies the program as a Portable Document File .
This covers both setting up and running of the program.
INTERCHEM is shipped with the following related programs.
INTERCHEM is shipped with the following data files:
INTERCHEM fragment catalogue (~400 structures optimised using MOPAC)
Parameter files for the molecular mechanics program ICMECH that is
incorporated in INTERCHEM.
Parameter file covering the 230 crystal classes, used by the
The INTERCHEM system, comprising all of the software and databases made
by Interprobe Chemical Services, is distributed world-wide under the
terms of the European
Union Public Licence (a form of Open Source licence) by:
Dr. Peter Bladon
Interprobe Chemical Services
Glasgow G66 4HX