I am trying to extract XYZ coordinates from a CIF file for a molecule to use in DFT calculations. I have Mercury and Vesta installed on my computer. Whenever I open the files, I get the following structure:
There seems to be molecular fragments and free hydrogen atoms in the molecular presentation (see the atoms marked in yellow). I understand that XRD is quite bad at locating hydrogens, and that sometimes you'll end up getting several positions of where the hydrogen is located.
How should I proceed in order to clean the file? I only want to have XYZ coordinates for each atom in the molecule without the fragments, is this possible to achieve in VESTA or Mercury?