Software Review June 97

Software review - DTMM v 3.0

Desktop Molecular Modeller (DTMM) Version 3.0 for Windows
Address enquiries to the supplier: Customer Service Manager, Electronic Publishing Oxford University Press Walton Street, Oxford OX2 6DP
tel +44 (0) 1865 267979 fax +44 (0) 1865 267990
Prices (excluding VAT and only a guide, contact supplier for current information):
DTMM itself �295 (if all additional libraries and utilities below are included �1115 )
Structure libraries �60 ~100 structures in each of: Biochemistry, Organic chemistry, Pharmacology, Biomacromolecules (includes polysaccharides, nucleic acids, proteins )
Structure Library �75 ~160 structures: Inorganic chemistry, and the Symmetry Operator Program
Additional DOS programs:
Symmetry Operator Program �150- applies symmetry operators and spacegroups to unit cell structures to generate crystals and lattices. Recognises all the standard space groups.
Protin �60- a utility for conversion of the PDB (Brookhaven) file format to DTMM

There was an earlier (non-windows version) which could be bought more cheaply for use in secondary schools. Site licenses are available.

DTMM is a molecular modelling program, allowing molecule synthesis, editing, energy minimisation, manipulation and display on an IBM PC compatible microcomputer.

Minimum System requirements: IBM 386 PC or compatible with a minimum of 4Mb RAM, DOS version 5.0 or higher, 'Microsoft Windows' version 3.1,VGA or SVGA monitor and graphics card, Microsoft MS-DOS standard mouse (or compatible)

What do you get in package? one highly packed 3.5" PC floppy disc containing 1075Kbytes, including some example molecules and fragments, and an A5 spiral bound manual with 170 pages. The manual has an index and a useful list of mostly historical references on molecular modelling. The tutorial section starts with 'Creating alanine and investigating chirality' and ends with 'Building a peptide and using secondary display styles' which continues with an investigation of the docking facility.

Installation: The manual sensibly advises one to make a backup of the original disc and use the backup for installation, which was easy, although it takes a while (I was testing it on a PC486SX 33MHz card in an Acorn StrongARM RISC PC, with 16Mbytes memory in the PC partition). It is clever enough to discover I do not have a math co-processor, which is recommended, especially for those who want to use the energy minimisation features.

File formats: DTMM reads crystal and orthogonal co-ordinate data from ASCII files in a format compatible with the CSSR (Crystal Structure Search and Retrieval) format. Files saved from DTMM can optionally include information on atomic charge and type. Protein Data Bank format files must be converted using the additional utility (Protin) not tested in this review. There is no mention of CIF files. Limits: DTMM allows up to 2700 atoms and bonds without a co-processor which makes it more use in a teaching than a molecular biology research environment.

Hardcopy output: is made via the 'Windows standard printing' devices, it may be monochrome or colour. The usual printing option allows saving to an Encapsulated Postscript (.EPS) file but this is merely a bitmap. The screen may also be saved to the Windows 'clipboard' or as BMP bitmapped files. (An earlier version used to produce real PostScript rather than these bitmaps which use a lot of disk space if you want high resolution; it is a pity this has not been carried over into Version 3.0. 'ATOMS' from Shape Software is still he only PC program I know of which makes 'real' PostScript output files, which have the advantage of small size and you can improve the resolution of your output merely by printing the file on a higher resolution printer. )

Display types:

stick,
ball & stick,
coloured line,
stereo (red/green and side by side)
space fill,
shaded fill,
coloured by electrostatic charge or charge distribution.

For those who are used to the older version, new features in DTMM 3.0 are:

docking of multiple structures
superposition
graphical display of energy terms during minimisation
calculation of volume & surface area
peptide build facility
display of secondary structural elements of proteins, helices as cylinders, sheets as large solid arrows
3 new display styles
1. charge distribution at van der Waals radius
2. space fill with light source shading
3. space fill with shading to represent electrostatic potential (needs 256 colours)
4. fuse ring command facility for changing the chirality of stereoisomers
5. annotate any display with text and arrows

DTMMShow is a utility to save 'Slides' to disc and replay later as a continuous demo. These just save the screen as bitmapped files (.BMP) so use a lot of disc space. No example files were supplied so I did not test this feature. I used an earlier version successfully for RAL Open Days some years ago.

Conclusions: DTMM itself is aimed at organic molecule synthesis, not at crystallographic structures. There is no display type showing parts of the structure as polyhedra, and no example datafiles of lattice structures supplied. (These may be included with the 'Inorganic' Structure Library which was not supplied for this review.) Plain DTMM could be used as a teaching aid for students of organic chemistry to learn about molecular modelling.
Kate Crennell
June 97

Page last updated 14 May 1997

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