Programs for Programmers


Desktop Molecular Modeller

Written and published by Polyhedron Software Ltd

NEW V4.2!

What is DTMM?

Desktop Molecular Modeller (DTMM)  is a simple-to-use molecular modelling program that enables you to perform powerful molecular synthesis, editing, energy minimizations, and display. The package, substantially enhanced from previous versions of DTMM, will run on any PC with Windows 95, 98, Me, 2000, NT, or XP.

First, a pretty picture...

Screen shot showing different molecule (lysozyme) display options

A screenshot from DTMM showing some of the different display options available. The molecule shown is lysozyme in all cases. You may notice a slight granularity in the shading in this and the other pictures - this is a byproduct of keeping the graphics files on the website to a reasonable size and is much less marked in DTMM itself provided your computer has more than 256 colours available. The program is currently in Atom mode with the Select Atoms option selected (see the depressed buttons on the top and right-hand button bars). This causes the information box seen in the 4th window to be displayed.

From the top left clockwise the windows show:

  • Ball and stick style. It's not too clear what the structure of the molecule is here!

  • Bonds only style with the Show main chain only option selected. It's now somewhat easier to see the secondary structure.

  • The display after defining a ribbon for the whole molecule (a two click operation). The secondary structure is now clearly visible. Atoms not included in the ribbon (i.e. not between the first and last a-carbon atoms) are shown as Ball and Stick.

  • Coloured Line style. The Zoom option has been used to examine a small portion of the molecule. The information box refers to the atom marked with the small yellow dot, which is selected simply by pointing to it., some details

Desktop Molecular Modeller operates by manipulating data loaded from structure files that are supplied in a format similar to the Crystal Structure Search and Retrieval (CSSR) format. There is no limit on the number of atoms and bonds that can be displayed except for the amount of memory available. Users of earlier versions of DTMM will be pleased to hear that the structure file format is unchanged.

Subject to this limit, any number of molecules may be displayed and manipulated, either in their own windows or several molecules in one window. The manipulations available include rotation of structures about any axis and their translation, magnification and reduction in space. A facility is provided that allows the continuous monitoring of the distances between up to eight pairs of atoms in differnt molecules or fragments. The monitor also displays a "goodness of fit" parameter: a measure of the root mean square distance in angstroms, between corresponding atoms when fragments are superposed. There are six display styles available, each of which can be customised, and in addition a display consisting of any combination of styles can be shown in side by side stereo. The following pictures were all produced using exactly the same data - a single menu click is all that is required to switch between them. A very simple molecule (acetone) is used here to keep things simple - see the above picture for displays involving a large number of atoms.

Picture of molecule (acetone) bonds only BONDS ONLY
Ball and stick representation of a molecule (acetone) BALL AND STICK
Coloured line representation of a molecule (acetone) COLOURED LINE (bonds coloured according to atom type)
Piture of shade fill representation of a molecule (acetone) SHADE FILL (rigorous hidden line removal based on intersecting spheres)
Picture showing charge distribution CHARGE DISTRIBUTION (a pattern of coloured dots is used to indicate the charge at the van der Waals radius)
Picture showing electrostatic as shade fill. ELECTROSTATIC (as SHADE FILL, but the darkness of shading of the molecule depends on the electrostatic potential of its constituent atoms)

Molecules can be viewed on-screen in any number of these display styles. Additional options include 'toggles' for display of shading, residue colour (for proteins), highlights, perspective, auto valency, and auto typing of atoms; removal of hydrogen atoms, and side chains (for proteins); and addition of axes, grids and atom identifiers to the displayed structure. The program can automatically determine the valency and type of each atom in the displayed structure. Structures can be re-oriented to offer the 'best view', or views along bonds or perpendicular to planes specified. DTMM can be also be configured to display atoms and bonds in any colour.

The most powerful features of the software are the editing and energy minimizing routines. These allow you to create new molecules, or to modify existing ones, on screen. Bonds can be continuously rotated, broken, lengthened, or shortened and atoms, fragments, and molecules changed, deleted, or joined together. This may be followed by an energy minimization which optimizes the geometry of newly created or edited molecules, by using an algorithm that calculates bond, angle, torsion, van der Waals, and charge energies to create a viable three-dimensional conformation.

View the minimizer window (31KB)

When minimization is complete, quantitative measurements of distances (in angstroms), angles, and torsion angles may be made. You can override the automatic assignments made by the minimization routine by setting the status of various toggles within the program. The minimization routine produces a report on the progress of the minimization and the assumptions used, which is produced in HTML format. The docking options provide facilities for minimizing the intermolecular energy of two or more fragments.

Peptide structures can be constructed rapidly from the program's built-in set of amino acid structures. You can choose from several pre-defined conformations, and you can define secondary structures and display them as ribbons.

View the Peptide Builder (15KB)

Screen images can be stored in either the standard Windows .BMP format or as JPEG files, and can therefore be used in many word processing, desktop publishing, and paint packages, offering the possibility of producing high-quality hard copy output. They can also be copied to the clipboard and pasted into another application; this method was used to create the GIF images in this document.

DTMM can print images of structures to any printer supported by Windows. Any screen display can be printed. Text labels can be freely added to any image, so that complete finished drawings can be created. By importing to suitable desktop publishing programs, therefore, you can incorporate DTMM images in documents for presentations or papers.

Most aspects of the display of structures in DTMM can be altered on screen via menus and dialog boxes, instead of editing configuration files. Your preferences are automatically stored by DTMM for use when you next run the program.

New features in V4.1

We have now implemented the most commonly asked for new features in DTMM. These are:

Read .mol files written in MDL format. This format is used by several other programs. DTMM will use bond types and charges defined in the file (if any). DTMM understands only a subset of the MDL format and will ignore anything it does not understand. If DTMM finds that a .mol file is not in the CSSR format it will automatically try to read it as an MDL format file. More details are given in the help file. We do not currently write MDL format files.

Force a particular bond to be either single or double. You will not normally need this feature as DTMM calculates bond types for you, however in ring structures you may need to use this feature to get double bonds exactly where you want them. User selected bond types are saved to .mol files.

Rotate or spin about a particular atom. This allows you to select an atom to be the centre of rotation.

Count selected atoms. This is an added piece of information in the "View selected atoms" dialog box. Depending on the technique you use to select atoms, you can for instance count the atoms in a particular fragment, or those with an x coordinate greater than 0.

Download a demo