Copy & Paste problem from ChemDraw

For the two structures in the attached ChemDraw file (test.cdx), if I obtain SMILES for them independently, and then put the SMILES as structures in MarvinSketch, they are two different ones (three chiral centers are different). However, if I copy both structures from ChemDraw and paste them directly into MarvinSketch. The resultant structures give the same SMILES.

Hi,

the following happens in the cases you have written.

When you use the smiles generated by ChemDraw, then that is containing the stereo information. The smiles importer can use the given stereo data and import the molecule correctly. When you simply copy from ChemDraw, and paste into Marvin, the used format for the transfer is the ChemDraw Sketch Format, that have some incompatible options with Marvin which can cause the problem you have described.

You can find the details on cdx file options in Marvin here.

Regards,
Istvan

Thanks for the reply, but I cannot see which import option affects the structures mentioned here.

Hi,

unfortunatelly i was worng, and there is a problem in the CDX import in Marvin. The next patch release that is scheduled to release in the second half of march will contain the fix.

Until that time, there are a few workaround possibility. One of them is to use copy as smiles from ChemDraw, or use other formats not cdx to transfer data between Chemdraw and Marvin. Another solution could be that, if you draw the specific up/down bonds to the molecule also, because if only the atoms contain the stereo information, the cdx import in Marvin will loose it.

Best regards,
Istvan