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:

enter image description here

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?

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    $\begingroup$ +1 Welcome to our new community and thank you for contributing your question here!!! We hope to see much more of you in the future!!! Please do look at the edits that I made though since there was quite a substantial amount of work that had to be done on your question. $\endgroup$ Commented May 16, 2021 at 16:30
  • $\begingroup$ Hi! :) Have you tried manually deleting the atoms after loading it into VESTA? (from the image attached it seems possible) or is it too tedious to do so? After deleting the unwanted atoms you can export it as an xyz file (VESTA) $\endgroup$ Commented May 16, 2021 at 19:29
  • $\begingroup$ @AnoopANair, Good suggestion, I think the same thing with Mercury. Maybe give it an answer? $\endgroup$
    – Cody Aldaz
    Commented May 17, 2021 at 9:20
  • $\begingroup$ @CodyAldaz Done!! :) $\endgroup$ Commented May 17, 2021 at 10:10
  • $\begingroup$ With Mercury you can sometimes select one of the representations and enlarge it, and then delete it. I'm not an expert on this, but I think it should be possible without too much trouble. $\endgroup$
    – MSwart
    Commented May 18, 2021 at 7:19

1 Answer 1



I'm an avid user of VESTA and haven't quite used Mercury. So I'll the steps to do it in VESTA (it's quite easy though)

Step 1: Open your file in VESTA

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Step 2: Choose the selection tool in the left panel. (highlighted in blue)

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Step 3: Click and drag to select the atoms you want to manipulate; Here the three top atoms

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After selection they are highlighted in yellow

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Step 4: Use the [Del] key to delete the atoms. And go to [file --> export] to export your structure.

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Step 5: Choose the appropriate extension (in you case the .xyz extension) to save it as an XYZ file.

enter image description here

Hope it helps :)


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