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I got hold of a CIF file for a material that I am interested in. I am trying to isolate the xyz coordinates of the molecules. However, when I open the CIF file in VESTA, I get a near-infinite periodic structure. See the attached image:

enter image description here

Furthermore, in VESTA, if I go to edit -> crystal structure -> systems and then choose molecule, I can reduce the system to a molecule. However, it looks quite weird, especially in regards to side groups. I believe that two possible representations of the side groups might have gotten super-imposed on each other. See the attached picture. Is there a way to fix this?

enter image description here

From the CCDC website, I was able to get a proper image of the unit cell I am looking for.

enter image description here.

The CDCC webpage with the CIF file is available in this link.

I am using VESTA and I have access to pyMOL, GaussView and the free version of Mercury. Ideally I would like to isolate the xyz coordinates of one of the dimers in the unit cell, is there an easy way to do this?

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    $\begingroup$ I think that you need to change the title of your post. It began as a visualization problem and ended with "how to export to xyz". Regarding this question, please take a look at a very similar post here $\endgroup$
    – Camps ♦
    Commented May 20, 2021 at 17:43
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    $\begingroup$ +1 But please do take a look at my edits so that others don't have to do this type of work in the future to keep our standards up. For example, the word "I" always has to be capitalized. $\endgroup$
    – Nike Dattani - No Free Time
    Commented May 20, 2021 at 17:54
  • $\begingroup$ Thank you for your edits. I will try to keep this in mind, English is not my first language so it is not always easy for me to formulate questions . I will try to not inconvenience the community with my errors again. $\endgroup$
    – Collodial_machine
    Commented May 24, 2021 at 9:31

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If you haven't figured it out yet here is what I would've done using mercury to get the xyz file of the dimer. There is some disorder in the crystal structure which I think means that there are partial occupations of molecules/atoms at different positions so you need to delete them to get only one of set of the dimers in the xyz file.

enter image description here

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    $\begingroup$ +1 Great first answer and welcome to our new community! We hope to see much more of you in the future !!! $\endgroup$
    – Nike Dattani - No Free Time
    Commented Jun 3, 2021 at 1:19

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