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I designed the $\text{MoS}_2$ molecule (bilayer), with polytype 2H in the VESTA. My goal is to draw the plans and axes of symmetry of the bilayer set. According to the information in the literature, this molecule belongs to the $\text{D}_{3d}$ point group. How can I draw and determine the planes and axes of symmetry in VESTA?

These are the parameters I used in VESTA:

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Mercury Attempt:

I exported the .vesta data to a .cif file.

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Table with space and point groups for $\text{MoS}_{2}$ (taken from https://iopscience.iop.org/article/10.1088/0953-8984/28/35/353002/ampdf) (see 2H phase for $\text{MoS}_{2}$):

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I do not know VESTA well enough to provide an answer for this program.

However because your data are about a crystal structure I suggest to export your model in the .cif format. CCDC's freely available version of CCDC's Mercury is able to read this file type, and add to its visualizations the symmetry elements of the unit cell (Display -> Symmetry Elements). There will be a new menu where you may choose among the symmetry elements the program is able to recognize, and how they are displayed:

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For example only the centres of inversion:

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The export options in Mercury include bitmap .png, ray-tracing PovRay .pov, and .vrml / .stl.

Given lattice constants and space group $P6_3/mmc$, do not forget to compare your model with the literature known models for example in the freely accessible COD about experimental data (entries #1010993, #1011286, #1531960, #9007660, #9009144); and consider contributing to its sibling TCOD about theoretical data and MPOD.

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  • $\begingroup$ Thank you for your answer. I tried to follow your suggestion and do it on Mercury. The objective is to draw the axes and the planes to prove that it is a $\text{D}_{3d}$ structure. To be a $\text{D}_{3d}$ structure, it must have 3 $\text{C}_2$ axes of symmetry. I put what I got on Mercury, in the post. The problem is that I am getting more than 3 axes of type $\text{C}_2$, and I should only get 3 axes of that type. Why do more than 3 axes type $\text{C}_2$ appear to me, when this structure should only have 3 axes type $\text{C}_2$ and what are those 3 axes in the last figure I put in the post? $\endgroup$
    – Jose Marin
    Commented Apr 13, 2020 at 18:03
  • $\begingroup$ In addition, the molecule you took from the COD library must have a bug in Mercury. In $\text{MoS}_2$ with polytype 2H, there is a bilayer and only Mo-S bonds are allowed. In the drawing you have in the images there are Mo-Mo bonds, which should not appear. $\endgroup$
    – Jose Marin
    Commented Apr 13, 2020 at 18:58
  • $\begingroup$ @JoseMarin We are sharing the same page here. Space group $P6_3/mmc$ (#194) is for unit cells of point group symmetry $D^4_6h$ (IT volume A1, p. 345, the 2006 edition). Yes, the diagram (e.g., img.chem.ucl.ac.uk/sgp/large/194az1.htm) indicates more than 3 $C_2$ axes perpendicular to $2/m$ and $6_3/m$ axes. $\endgroup$
    – Buttonwood
    Commented Apr 14, 2020 at 20:55
  • $\begingroup$ @JoseMarin Mercury is developed by CCDC; contrasting to ICSD with more inclination for organic, and metalorganic compounds. So its geometric approach draws lines between atoms if their distance is quite less than the sum of the van der Waals radii. With S 1.80 A, Mo 1.90 A, d(Mo-Mo) = 3.15..3.16 A which is lesser than 2 x 1.90 A. With the input given in your question, I was not able to reproduce the trigonal prisms of your question (vesta 3.4.8); indeed, pressing the «remove duplicate atoms» with default 1e-006 leaves only one Mo and one S (still no prisms). $\endgroup$
    – Buttonwood
    Commented Apr 14, 2020 at 21:04
  • $\begingroup$ @JoseMarin Loading one of the COD entries (#1010993, #1011286, #1531960, #9007660, and #9009144) as .cif into Vesta however yielded the prisms of the original question within a blink of an eye; each of them require only one Mo and one S for the model's definition. $\endgroup$
    – Buttonwood
    Commented Apr 14, 2020 at 21:09

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