3d structure:same from hydrogenized and dehydrogenized mol ?

Hi,





I use the clean method with parameters (3,"S{conformers}") to generate 3d structures. It seems that, for the same structure, the number of conformers generated is not the same if this structure is first hydrogenized or not.





Is that normal ?





Vincent B

Hi Vincent,





This behavior will very likely change in the future. however, in the current version, Hydrogens are added during the Clean3D process only if they are necessary (e.g. for ensuring chirality). For more accurate results I suggest adding explicit Hydrogens before the Clean3D process and using more tight optimization criteria might also be beneficial ([L]2 or [L]3). The default parameters are for a guessed good tradeoff between speed and accuracy but power users may play with the parameters to adjust the process for their need.





Best wishes,





Ödön