Tryout version of Marvin: aromatic rings not saved

User b814ae3513

03-02-2011 13:03:37

If I create a compound with aromatic groups in Marvin Sketch Online Tryout version and save it as a pdb file, when the file is reopened, the aromatic groups are no longer shown correctly (i.e., with a double bond to one O atom). Instead, the aromatic groups now have the single-bonded C atom. Is this a bug? If not, is there a way to correct this behavior? Thank you.


P.S.: The doubles bonds are shown correctly if the file is save has .mol (Sybyl compatible file). So i think the problem is only by saving in .pdb?

ChemAxon 5433b8e56b

09-02-2011 13:49:24

Hi,


First of all sorry for the late answer.


This is not a bug. The pdb format does not store the bond information at all, and the import of the pdb format only guess the bond information from the geometry of the atoms.


Regards,
Istvan