Software and File Handling Details:

CHEMMOL is a simple , small, executable DOS programmme which will be offered free for individual exploratory use, initially on PCs. A copy of Chemmol , installation and operating instructions along with a test series of original and converted mol files.will be made available(click here) .

It should be copied to a new directory(we use cmol) and all files to be converted should be copied to the same directory. Converted files (we use a prefix dc) will be written in the same directory. Filenames must comply with DOS rules and be a maximum of 8 characters plus the 3 letter extension .mol.

The DOS command , from directory cmol is

cmol>chemmol filename1.mol dcfilename1.mol

so that

cmol>chemmol heroin.mol dcheroin.mol

will produce the display coordinate(DC) file corresponding to heroin.


We would appreciate it if users would report to us the number of successful conversions carried out and , more importantly, please supply details of any molecular conversions which are deemed incorrect or partially incorrect ( We know of some, including the disaccharide above, so no prizes are on offer!). The best way to do either of these is to ftp both the initial 2D .mol file and its convert (DC) .mol file(see below for explanation of our conversion nomenclature). Anonymous ftp directories have been established at [ and] for input of both successes(OK) and failures(BAD). If users cannot use this ftp facility then we will try to process PC disk copies of .mol files or the same files incorporated in Email or as MIME attachments to Email. These files and results mayl be made publicly available, unless specific requests for confidentiality are made.


This version of CHEMMOL is a prototype, so users should clearly recognise its limitations. No responsibility is taken for any consequences arising from its use . It can only handle "simple molfiles" containing explicit bonds. So structures containing superatoms, characterstrings or R groups need to be depicted as simple mol files. The "draw stick structure" command in CHEMWINDOWS v3.1 could be used , for example, to do this.


Dr. Bernard Blessington, Bradford University,

Department of Pharmaceutical Chemistry, Bradford BD7 1DP. England

Tel. +44(0)1274 384704 Fax +44(0)1274 305340

Email B.Blessington@Bradford.AC.UK


Dr. Roger Sayle, Glaxo Research and Development,

Gunnels Wood Rd., Stevenage, Hertfordshire, SG1 2NY.

Tel. +44 (0)1438 763246