multiple molecule/structure .sdf file

How does one save multiple molecules in a single .sdf file?


I had several molecules I had sketched and saved but apprently the ChemAxxon reactor thinks they are one reactant instead of two.


How does one save them in such a way that the reactor and other


programs recognise the constituent molecules/structures as distinct?





Do I have to simply do a UNIX 'cat' command and concatenate them?





Thanks,





Kelsey

Hi Kelsey,





1. Draw the first molecule in msketch.


2. Save to an sdf.


3. Select new/clear desk to get an empty canvas.


4. Draw the second molecule.


5. Select save. Now msketch will ask you if you want to overwrite the molecule in the sdf or append. Select append.


etc.





Simply cat-ing molfiles would also work, because ChemAxon tools can read concatenated molfiles, but they are not proper SD-files, and may not work with other programs.





To construct a proper SD-file, I recommend molconvert, which comes with Marvin:





http://www.chemaxon.com/marvin/doc/user/molconvert.html





You should use a command-line like this:

Code:

$ molconvert sdf a.mol a1.mol -o output.sdf

Best regards,


Szabolcs