INTERCHEM

INTERCHEM is a general purpose molecular modelling program written by Robin Breckenridge and Peter Bladon of the University of Strathclyde.

Design Criteria

• Attention has been devoted to making the program accessible to the relatively inexperienced user.
  
• It should be possible for beginners to obtain useful results without extensive training.
  
• It should be useable by chemists of all sorts (i.e. it should attempt to bridge the gaps between, for example, theoretical chemists and organic chemists).
  
• It should facilitate access to many of the well known packages (e.g. MOPAC) which are available for computational chemistry.
  
• Menus should be as explicit as possible
  
• Only minimal knowledge of UNIX should be needed.

Main features of INTERCHEM

• DISPLAY MODES FOR STRUCTURES (simple modes)
  • Wire frame display.
  • Atom-numbered wire frame display.
  • 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.
  • Provision is made for viewing stereo images if the necessary equipment is available (e.g. CrystalEyes hardware).
    
• 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

  For display modes not involving the lighting effects, manipulations occur in real time, even for structures having large numbers of bonds and atoms. With structures involving lighting models, rotations and scalings occur at acceptable rates, but the rate is dependent on the number of atoms (and on the platform on which the program is mounted).
  

• 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 bond-lengths
  • Calculate non-bonded distances
  • Calculate bond angles
  • Calculate torsion angles
  • Write file of bond lengths, bond angles, and torsion angles
  • Write listing file of co-ordinates and connectivities
  • Identify chiral centres
  • 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.
    
• 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 methods:-
    • Three point fit
    • Least-squares fit of between 3 and 25 atom pairs
    • Least-squares fit with fragment rotation
      
• STRUCTURE EXCHANGE AND COPYING
  • Any one of the structures A, B, C, D may be copied into any of the others.
  • Any pair of structures chosen from A, B, C, and D may be exchanged
    
• STRUCTURE MERGING
  • The pairs of structures A and B, or C and D, may be merged to give a composite structure.
  • 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 interactions.
  • 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
    
• STRUCTURE BUILDING
  • 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 fragment.
    • 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 coordinate
    
• STORAGE OF STRUCTURES
  • INTERCHEM has a defined format for storage of structures, which 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 programs MOPAC, AMPAC
    • The ab initio program GAMESS (UK Version)
    • The molecular mechanics programs PIFF and MINIMAX
    • The distance geometry program DGEOM
    • The structural data output from these programs may be read back into INTERCHEM
    • Solvent-accessible surface displays using Connelly's program may be produced from INTERCHEM structures, using a version of the program bound into INTERCHEM.
      
• SHAPES AND POTENTIAL OPERATIONS
  • A facility is provided to display the accessible surfaces of molecules coded to show the potentials at the surface due to charges on the atoms.
  • The 3-dimensional isopotential surfaces due to the atomic charges in molecules may be drawn, and potential contour maps may also be produced.
  • 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).
  • The potentials surrounding molecules due to the charges on the atoms may be displayed projected onto transparent encompassing spheres or ellipsoids.
    
• SPECIAL FACILITIES FOR EXAMINING PROTEIN AND NUCLEIC ACID STRUCTURES
  • Besides the normal display methods there are special functions available including:-
    • Colour coded wire frame display to show amino-acid or nucleotide components.
    • 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).
    • Display of protein structures in cartoon form
  • There are functions to analyse the data contained in protein structure files in special ways:-
    • Torsion angles analysis.
    • Ramachandran and Balasubramanian plots to show protein secondary structure.
    • A method to find significant sites in a protein structure.
  • Protein structures may be truncated selectively,
    • by selecting residues to be retained
    • by retaining all of the structure within a defined radius.
  • Methods are provided to predict protein secondary structure features starting from the amino-acid sequence; four established methods are used, and the results from all of these may be compared.
  • The predictions may also be edited by the user, and the resultant consensus prediction preserved in a torsion angle file.
  • The torsion angle files can be used to build peptide sequences into standard INTERCHEM structures automatically.
    • There is a choice of preparing:-
      • Backbone only structures,
      • Structures containing all atoms except hydrogen,
      • Full structures containing all hydrogens.
        • Peptide structures containing hydrogens can be made in:-
          • Un-ionised form,
          • Zwitterion form
          • Forms expected at different pH values.
      • Provision is made for selectively forming S-S linkages
      • Provision is made for forming cyclic peptides.
    • The structures containing hydrogen may be submitted for structure optimisation using the program PIFF.
    • Alternatively, structures may be submitted to the distance geometry program DGEOM via special files.
  • A comprehensive package for the interactive investigation of protein homology is provided.
    • A maximum of 60 sequences containing up to 400 amino-acid residues may be compared.
    • Pairs of sequences may be aligned using an implementation of the Needleman-Wunsch algorithm.
    • In addition manual alignment of whole blocks of sequences is catered for.
    • Full 'spread-sheet' type operations are also provided; sequences may be moved, copied, edited, and stored.
    • Sequences may be randomised (to test for significance of homology),
    • Sequences may be reversed (to test for sequence palindromy).
    • A method is provided for examining evolutionary relationships between groups of highly homologous sequences.
      This searches for (apparently) simultaneous changes in residues in sequences,
      to find regions in a protein which may be of importance to the function of the protein.
    • Facilities are provided to translate DNA and RNA sequences into protein amino-acid sequences.
      • Choice of reading frame is provided,
      • In survey mode all three reading frames are tried, and a report of the maximal peptide length is given.
      • The complementary nucleic acid strand may be investigated as well.
  • If a version of the Brookhaven Protein Data Bank is available on the machine (or via a network), then the auxiliary program PROTEINS can be used from within INTERCHEM, to translate the data into files in standard INTERCHEM format.
    • PROTEINS may also be used from a terminal connected directly to the workstation, or from terminals connected to it via a network.
      
• SPECIAL FEATURES FOR THE EXAMINATION OF CRYSTAL STRUCTURES
  • Data files from the Cambridge Crystallographic Data Base may be loaded into the system.
  • 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 electric vector.
  • 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.
    
• MISCELLANEOUS FACILITIES
  • Access to UNIX operations
  • Display testcard for camera setup
    
• PROGRAM CONTROL
  • With the large number of features and functions provided in the program, its control might be thought as likely to present some problems. However, it has been designed to be easy to use.
  • Control is achieved by use of very explicit pop-up menus. These guide the user to those operations which are permissible at each stage.
  • Structure manipulation and some other features are controlled by the use of cursor picking on static menus, and in some cases the functions of these menus is duplicated by the function keys.
    
• COMPUTER REQUIREMENTS
  • Hardware
    • The program is designed to run on current Silicon Graphics workstations but will work on many of the older models.
    • The following should be regarded as minimum requirements:-
      • 32 Bytes of memory (more memory is an advantage)
      • 2 GByte disk (larger disks are needed if extensive databases are to be stored)
      • DAT drive (preferred) or QIC drive (needed for loading software, but not needed if network access is available).
      • 24 bits graphics colour planes (used as 2 x 12 bits, i.e. double buffering is used),
      • 24 bits Z-buffering (the "software Z-buffering" provided on Indy XL machines is adequate; on the O2 machines the "unified" memory provides the Z-buffering).
      • 1280 x 1024 resolution screen is needed (this is essential).
    • The program will run succesfully on the following machines:-
      • Indigo XS, XS24, XZ, Elan, Extreme
      • Indigo2 XL, XZ, Extreme, Impact systems
      • Crimson XS, XS24, XZ, Elan, Extreme
      • Indy XL,XZ
      • O2 systems
      • Octane systems
    • Although the requirement of 24 bit graphics is stated above, the program will work on 8-bit graphics systems such as the Indy-8-bit. (there is some degradation in colour rendering performance however).
    • It is NOT SUITABLE for the entry-level Indigo and Indy having 1024 x 768 resolution screens.
  • Software
    • The current version of the program is designed to use version 6.5.x of the IRIX operating system, but will work on earlier versions .
    • For compilation the UNIX f77 (Fortran) and cc (C) compilers must be available.
    • For convenience the system is shipped with executable versions of programs for versions 6.5 of the IRIX system in addition to full source of all the programs.
  • Special systems.
    • If you have an older SGI system, it is still possible to use INTERCHEM. Contact us with your requirements
      
• DOCUMENTATION
  • INTERCHEM is fully documented in a 250 page manual. The functions of the program are also detailed in HTML format files, for online viewing.
    
• ANCILIARY PROGRAMS
  • INTERCHEM is shipped with the following related programs.
    • PROTEINS (for format conversion of Brookhaven files)
    • PIFF (molecular mechanics program)
    • ICMECH (molecular mechanics program)
    • CONVERT (general file-format-conversion program)
    • THREEDOM (3D-Database searching program)
    • AUTOBUILD (program to automatically generate large number of structures)
    • CHEMSPREAD (statistical spreadsheet package for analysing quantum mechanical data on series of compounds)
    • PRESTO (program to correlate protein sequences)
    • FINDSEQUENCE (program to access local copy of PIR protein sequence database)
      
• DATA FILES
  • INTERCHEM is shipped with the following data files:
    • INTERCHEM fragment catalogue (~400 structures optimised using MOPAC)
    • Eighteenlarge databases totalling 4.3 million small molecule structures in INTERCHEM format for use with THREEDOM:
    • Modified version of PIR protein database for use with FINDSEQUENCE
      
      
• AVAILABILITY
  • The INTERCHEM system is distributed world-wide under license by:
    
    • Dr. Peter Bladon
      Interprobe Chemical Services
      Lenzie Kirkintilloch
      Glasgow G66 4HX
      Scotland
      
      Telephone:- 0141-578-1109 (+44-141-578-1109)
        Facsimile:- 0141-776-7712 (+44-141-776-7712)
      Email:- cbas25@strath.ac.uk
      
• FURTHER INFORMATION
  • Contact Dr. Bladon at the above address or by email
    
• PRICE
  • The price of a site license for the INTERCHEM system (all programs and databases) is:
    • £2500 (UK) for Industrial and Government organisations
    • FREE to academic and other not-for-profit (i.e. charitable) organisations

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  Revised 18th June 2007