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).
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.
- Select the formula. Press Cmd-U. Pick the red color. You will see a number appearing near each atom.
- Double click the structure. A dialog appears. Move the dialog to uncover the formula beneath it. Resize the dialog to read all the text displayed. The text you see is the mol file.
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 ...........
- Notice the atoms no. 12 and 28. In the original ChemDraw picture they were not atoms, but groups. Go to the 12th line in the atom list (contains -18.9129) and change the “C” into a “d” and the next two spaces at its right into “e” and “x”. The trick is not to delete nor to add characters.
- Close the dialog and see the effect.
- Now double click again and repeat for the line 28 in the atom list (contains -38.5674).
- We want to change the shape of some bonds. Let's start with the bond connecting atoms 3 and 11.
- Go to the line, in the bond list, beginning with “11 3 1 6” and change it into “ 3 11 1 1”. In the same way, change the bond between atoms 32 and 24, from “32 24 1 6” into “24 32 1 1”.
- Close the dialog again.
- We reached the maximum we could do within the definition of mol file. To change the bonds 10-11 and 31-32 we need to go outside the standard. Stop here if you want to regenerate the mol file from the structure, continue otherwise.
- In the lines corresponding to the bonds 10-11 and 31-32 change the zero in the 4th column into a 2.
- Close the dialog. To hide the numbers, right-click the structure and, from the contextual dialog, select the last command.