Adding Hydrogens change molecule coordinates

Hello,

I'm using the 5.5 version of JChem and i'm trying to put explicit hydrogens in my sdf files, using standardizer.

I'm running the following command:

standardize 0Z1_1ela_A.sdf -c add_H.xml -f sdf -o 0Z1_1ela_A_with_H_command_line.sdf

In add_H.xml, I have only one action:

<AddExplicitH ID="AddExplicitH"/>

Well, the hydrogens are added... the problem is, I have lines which were like this:

41.0260   23.4570   37.5520 C   0  0  0  0  0  0  0  0  0  0  0  0

which transform into:

2.8494    1.7190    3.9279 C   0  0  0  0  0  0  0  0  0  0  0  0

When I'm utilising the GUI to do the same thing (Structure->Add->Add explicit hydrogens) all is running fine and the coordinates are untouched. (see 0Z1_1ela_A_with_H_marvin.sdf)

So, is there a way to prevent this behavior from command line?

Thanks,

Florent.

Hi Florent,

Our Standardizer experts are on Holiday now.

Until they will answer your quiestion - regarding the possibilites of switching off cleaning during adding explicit H - I would recommend using 'molconvert' to add hydrogen to your molecules.

Example:

molconvert mol:+H 0Z1_1ela_A.sdf 

Best regards,

Viktoria

Works like a charm this way.

Thanks, and happy holidays to you and ChemAxon team !

Florent.