Showing all H-Atoms when importing SMILES in MarvinView

Hello,

Im trying to get any H-atom appear when importing e.g. n-hexane (SMILES: CCCCCC). Using mview_param("explicitH", "true"); has no effect - only a chain of C-atoms is shown. It is also not choosable in viewing mode... Can anybody help me?

regards,

Maik

Hi Maik,

you have two options, if you only want to display the hydrogens, then use implicitH parameter with "all" value.

If you want to add the hydrogens to the structure itself also, then use the following two parameter:
 - explicitH with value "true"
 - importConv with value "+H"

The first version only shows the hydrogen, but the second modifies the molecule structure itself, and adding the hydrogens to the representation.

Information about the parameters can be found on this page.

Information about the difference between implicit and explicit hydrogens in Marvin can be found on this page.

I hope that helps, but if you have further questions do not hasitate to ask.

Best regards,
Istvan