# Structure using symmetry

**URL:** <https://discuss.avogadro.cc/t/structure-using-symmetry/3472>\
**Category:** General Discussion\
**Created:** [April 9, 2021, 11:35pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472 "2021-04-09T23:35:35Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![Rajan](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/r/b5ac83/32.png) [@Rajan](https://discuss.avogadro.cc/u/Rajan)\
**Post date:** [April 9, 2021, 11:35pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/1 "2021-04-09T23:35:35Z")

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I am new to Avogadro, I believe the software is capable of creating the whole structure if just provided with the symmetry atoms and assigning the symmetry of the molecule. The output can be seen in the MacMolplt. I tried doing it but did not get any success, I would appreciate any help, to walk me through the steps. I am trying to model Ni(COD)2.

PS: I am not a chemist, a computaional person.

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**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [April 12, 2021, 6:18pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/2 "2021-04-12T18:18:48Z")

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At the moment, that’s not possible, but should be fairly easy to add to Avogadro2, which has strong symmetry support.

Do you have a specific example we can try (e.g., the symmetry-reduced Ni(COD)2)?

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**Author:** ![Rajan](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/r/b5ac83/32.png) [@Rajan](https://discuss.avogadro.cc/u/Rajan)\
**Post date:** [April 20, 2021, 4:35pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/3 "2021-04-20T16:35:46Z")

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Thank you for the reply, I am interested in the Ni(COD)2, it would be great to get an input generated based on the symmetry in Avogadro/ 2 which I can use further to feed to GAMESS and get a model output. I would really appreciate the help.

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**Author:** ![Rajan](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/r/b5ac83/32.png) [@Rajan](https://discuss.avogadro.cc/u/Rajan)\
**Post date:** [April 22, 2021, 6:23pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/4 "2021-04-22T18:23:34Z")

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Hello Dr. Hutchison,

We can try symmetry-reduced Ni(COD)2, Please let me know what steps to follow, or if there is any module/ article I need to refer to.

Thank you.

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**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [April 23, 2021, 3:05am UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/5 "2021-04-23T03:05:58Z")

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This feature does not yet exist. It would probably take a few weeks before it can be implemented.

If you want to create a full \ce{Ni(COD)2} molecule, it’s a bit tricky.

Here’s an example (\ce{S4} symmetry)

> **[Ni(COD)2 XYZ coordinates - Pastebin.com](https://pastebin.com/8ak45uMB)**
>
> Pastebin.com is the number one paste tool since 2002. Pastebin is a website where you can store text online for a set period of time.

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<div class="post-metadata">

**Author:** ![Rajan](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/r/b5ac83/32.png) [@Rajan](https://discuss.avogadro.cc/u/Rajan)\
**Post date:** [April 23, 2021, 4:37pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/6 "2021-04-23T16:37:35Z")

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Dr. Hutchison,  
Thank you for the file. I have a question, what we doing here is creating a cartesian coordinate file for the reduced structure of Ni(COD)2, why cannot we obtain similar results with the normal structure?

I am trying to reproduce the same results from this paper.

[Theoretical study on the reaction mechanism of “ligandless” Ni-catalyzed hydrodesulfurization of aryl sulfide](https://www.researchgate.net/publication/320907155_Theoretical_study_on_the_reaction_mechanism_of_ligandless_Ni-catalyzed_hydrodesulfurization_of_aryl_sulfide)

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<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [April 23, 2021, 6:16pm UTC](https://discuss.avogadro.cc/t/structure-using-symmetry/3472/7 "2021-04-23T18:16:54Z")

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> [@Rajan](#):
>
> the reduced structure of Ni(COD)2, why cannot we obtain similar results with the normal structure?

I’m not quite sure what you mean. The link I provided is to coordinates of a symmetric \ce{Ni(COD)2} structure. I don’t know what you mean by to “normal” or “reduced.” There are multiple possible meanings to those words.
