Problem Displaying smiles in MarvinSketch

When I read in the following smiles from a textarea as cxsmiles using setMol(s,'cxsmiles'),

[H][C]([H])[H]

marvinsketch automagically makes it a radical.

However, when I open the same smiles string with the menu File->Open, it doesn't show the radical electron.   In this case I saved as a cxsmiles before hand.  Is there some setting or something I'm missing?  I'd like setMol to behave like File -> open (i.e to not show the lone electron).  I understand this doesn't make chemical sense...I'm making test and quiz questions.

Thanks

Carl

Hi Carl!

The correct behaviour is when the radical is added, I can not even reproduce the format without the radical. Is it possible that you are using an older version of Marvin Sketch?

Marvin Sketch performs an automatic valence check on the imported molecule. Since a Hydrogen is missing from the definition [H][C]([H])[H] and with adding brackets to the Carbon atom it is declared that adding implicit Hydrogens is not allowed, the valence is corrected by adding a radical.

If you use format [H]C([H])[H] then instead of the radical an implicit Hydrogen will be added to the Carbon atom and by setting in the menu View->Implicit Hydrogens->Off this implicit Hydrogen will not be displayed. I hope this answers your question.

Best regards,

Zsuzsa

Armed with that info I got it working flawlessly! Thanks very much!

Carl

Hi, I want to tag my question to this thread since it is related to radical as well.

I have a smiles like Clc1c[nH]c(=O)c2ncc[n]12, it was display as radical form. If I remove bracket around the last 'n" as Clc1c[nH]c(=O)c2nccn12, it displays fine. Any idea how to resolve this?

 

Thanks

Hongzhou

Hi,

This is a bug as there shouldn't be any radicals on the nitrogen. We will fix it in Marvin 6.0.

Regards,
Domi

Thanks for confirmation. Do you have a timeline for 6.0 release? If it takes long, is it possible to release a patch?

Hi,

Marvin 6.0 is estimated to be released in may. Marvin 5.12 release will be soon in beta phase but at the moment the release date is unknown. This bugfix will be included in 5.12.1 which's release date can be discussed right after the 5.12 release.

Regards,
Domi