Manipulating a mol file

The snapshot below was taken from iNMR version 2.3.3. It illustrates that not all information can be kept when transforming a ChemDraw file into a mol file. At the right you see the original ChemDraw picture. To generate the picture at the left the user opened the .cdx file directly with iNMR and let iNMR do the drawing. How many differences can you spot? This brief tutorial will explain you how to overcome these differences. FTF: download the ChemDraw file. (alt-click the link). Now be sure to have at least version 2.3.4 of iNMR. This version is a little smarter when it comes to draw the OHs. Also be sure to have OpenBabel installed. Why ?? OpenBabel translates between many formats of chemical files. If you don't want to install OpenBabel, download this mol file. (scroll down this page to continue).

same structure as mol file and ChemDraw picture

Open any spectrum with your recent version of iNMR, then open the ChemDraw file (it's called tutorial.cdx). You should see the same formula as above. The OHs are correct, but other details are still wrong. You can correct them by editing the mol file. What's a mol file? It's a standard way to describe a structure. It's also a text file. iNMR converts all ChemDraw files into mol files, because it's the only format it can draw. The text of the mol file is then encapsulated into the spectrum and interpreted each time the latter is drawn.


babel.cdx
 OpenBabel10140718172D

 32 33  0  0  0  0  0  0  0  0999 V2000
   27.1533  -21.0964    0.0000 O   0  0  0  0  0
   28.5180  -23.4696    0.0000 C   0  0  0  0  0
...........

 
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