Bugs in MarvinView

1. Compounds with tin or silicon that have less than four bonds to


silicon or tin atoms - the software doesnt add the hydrogens to the tin


or silicon atoms when it saves the sdf file after the explicit hydrogens


have been added


2. Compounds with nitrogens in 5 membered rings (with only 2 bonds to


non hydrogen atoms)- again the software fails to save the hydrogen when


the sdf file is saved.

We will investigate it.

I cannot reproduce this problem. I think I've tried all possible definition of explicit hydrogens, and it is always saved to the SDFile (both from Marvin Sketch and Marvin View).





Would you please write me the steps you did, then I can follow them. Please also indicate the version number of Marvin you use.





Thanks.

I think the problem for the nitrogens was that the original smiles didnt have the hydrogens explicitly defined for the aromatic nitrogens with a hydrogen attached. Marvin would let you add the explicit hydrogens but then it wouldnt output the hydrogen to the sdf file. In fact the hydrogen in question would revert back to an implicit one after the sdf file was created. If i used a correct smiles to begin with, this doesnt happen.





I was also wondering about Silicon compounds.


For 4109-96-0, Smiles = [Si](Cl)Cl


Marvin wont add hydrogens- is the original smiles wrong as well?

My marvinview version is 4.1.10

Fist of all, the correct smiles is as follows:





[SiH2](Cl)Cl or Cl[SiH2]Cl





On the other hand, I still could not detect the missing hydrogen atom problem in sdfiles. If you paste the original smiles - [Si](Cl)Cl - into Marvin, two radical electrons are shown, and it is true, that if I add two explicit hydrogens, these radicals will remain on the Si atom, and are also exported into the SDFile, but the explicit hydrogen atoms are exported, too.





Anyway, it is better to start from a correct smiles, then these problems will not appear :)