Conversion of Smiles into Marvin in CDD

Hi Developers,

I have a client, who uses ChemDraw to draw structures which he
converts to Smiles strings and transfers them into Collaborative Drug
Discovery tool. I ask this on his behalf because CDD uses ChemAxon
technologies and the problem he is facing is that when he imports these
very smiles strings into Marvin in CDD, the orientation gets disturbed.

Any ways to get around this problem?

Please advice,

anu

Hi Anu,

If your client is copying the structure as SMILES, the atomic coordinates are lost,
and during the paste (or import) action into Marvin, the 2D clean generates new
coordinates. Therefore the original orientation "gets
disturbed" of course. If you want to copy the molecule as it was drawn
in ChemDraw, you have to copy (or export) it in a format that stores the atomic coordinates, e.g. as CDX- or MOL file.

On the other hand, if this issue is about the quality of the 2D cleaning, please send us the SMILES you expect to be better cleaned. Thanks.

Best regards,

Akos