Subject: file format?

From: Rajarshi Guha <[email-masked]>
Date: Wed, 28 Feb 2001 09:57:12 +0530 (IST)

Hi,
  I was using the software package DTMM (for windows) to draw some
molecules. After saving them I see that it uses a .mol suffix. But babel
does'nt seem able to convert them. I've been using the mol or mol2 types
Could anybody tell me what file format DTMM uses?
TIA

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Rajarshi Guha                       | Genius is pain.
Dept. of Chemistry		    |
IIT Kharagpur.                      |         -- John Lennon
		                    |
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web  : www.psynet.net/jijog         |
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From: "Tamas E. Gunda" <[email-masked]>
Date: Wed, 28 Feb 2001 10:32:50 +0100

Dear Rajarshi,

You mean the DTMM = Desktop Molecular Modeller? I have an older version and it uses a simplified format of CSSR.
Don't be confused with the .mol suffix: a number of very different file formats uses this suffix.

Open the file with any text editor. If the beginning looks similarly like this:

                                         1.000   1.000   1.000
                       90.000  90.000  90.000
  60

  61 C       0.28000  -3.13070  -3.30400    2   6  32   0   0   0   0   0
  62 C       1.61320  -3.51880  -3.09460    1   3  33   0   0   0   0   0

then it is CSSR file. 

Hope this helps

Tamas

------------
Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
University of Debrecen, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 512 900/2472
fax: (+36-52) 512 914
e-mail: [email-masked]
home-page: www.klte.hu/~gundat/gunda.htm

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From: "Bruce. Tattershall" <[email-masked]>
Date: Wed, 28 Feb 2001 10:54:06 +0000 (GMT)

On Wed, 28 Feb 2001, Tamas E. Gunda wrote:

>   You mean the DTMM = Desktop Molecular Modeller?  I have an older
>   version and it uses a simplified format of CSSR.  Don't be confused
>   with the .mol suffix: a number of very different file formats uses
>   this suffix.

That is very useful information:  babel will convert from dtmm format, 
treating it as cssr.  However, I have just tried converting an .xyz file
to .cssr format using babel, and find that dtmm will not read the resulting
file.

  Bruce

[email-masked]
    Dr. B.W. Tattershall    Department of Chemistry
    University of Newcastle    Newcastle upon Tyne
    England

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From: "Bruce. Tattershall" <[email-masked]>
Date: Wed, 28 Feb 2001 10:23:27 +0000 (GMT)

On Wed, 28 Feb 2001, Rajarshi Guha wrote:

> molecules. 

The answer appears to be 'a very fussy one'.  My experience is that the
file format, while it is plain text, has to have the numbers in strictly
defined column positions.

For a modest sized molecule, it is easy to get from dtmm format by using
a text editor to hand edit the file to .xyz format, which can then be   
translated using babel or molden.  You just need a text editor which
preferably can do rectangular block copy, delete etc., i.e. is designed for
column-oriented text.

To go to dtmm format, I eventually became desperate enough to write a
program, todtmm.for, which I attach as plain text.  This reads a coordinates
file which is in relatively free format, so can easily be generated from
an .xyz file by hand editing.  This format is described in the program
comments.

My coordinates file format was originally designed for input to my
programs bangl and tangl, to tabulate bond lengths and angles, and
torsion angles, respectively.  I also attach these programs, in case
they are of any use to you.  They produce identical results to the
distance or angle tables in Gaussian output, or individual measurements
using molden (but different to Rasmol or the Chime plugin, which seem to
suffer from rounding errors).

No guarantees given!  Bangl and tangl have been in use for many years,
but todtmm is much less tested, as I have now given up using dtmm in favour
of software which can read mdl .mol files etc.

Bruce Tattershall