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arohl / gdis

A visualization program for the display, manipulation, and analysis of isolated molecules and periodic structures
GNU General Public License v2.0
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is there a way to add hydrogen atoms to CIF file? #49

Open haoasakura12 opened 3 years ago

haoasakura12 commented 3 years ago

Dear,

I'm trying to use GDIS to create an input for Quantum Espresso. The CIF file has an organic molecule, but it was obtained without the hydrogen atoms. Is there a way to use the add atoms function (or another one) to introduce the H atoms in the correct position? I've tried but the atoms were far from the correct position

Thanks for your help

arohl commented 3 years ago

The add atom functionality is very basic. I have added hydrogens in the past by adding an atom as you say above and then use the atom coordinate inspector to change the coordinates of the atom so that it looks reasonable. This is fine if you are doing a force field optimisation as the FF will pull it to a good position easily. It is not a good use of QM though.

I think I used to use Mercury to do this

haoasakura12 commented 3 years ago

Thank you for your answer! Is Mercury a free or paid software to do this function?