To some extent the removal of (non translation) symmetry might help. Then different central atoms become inequivalent. Then you redefine the atom type of the central atoms for the polyhedron under consideration (e.g. different atom type) and can define the polyhedron properties for the new atom type. If you show more than one unit cell, you might have to define a supercell (unit cell transformation). Apparently there is no option like "convert to molecule", where all atoms currently shown are coverted to a molecule without translation symmetry. This exists for other programs, but apparently not for Vesta.

Additional detail motivated by an additional response which has been deleted in the meantime (changed August 21th 2019): I was making a difference between translation symmetry and rotational symmetry. The translational symmetry is retained upon using the "remove symmetry" option (execept for centering translations). I was in particular referring to the case where you e.g. show 2 x 2 x 2 unit cells. Changing the atom color after having removed symmetry, affects all atoms which are still equivalent by translation of the initial unit cell. In the software crystalmaker there is the option crystal->molecule, which works differently (all atoms shown at the moment get independent).

I have just discovered that there is the option "molecule" in vesta (menue Unit cell/system). But switching to this retains only the different atoms in the unit cell. Therefore I see only the solution of using a supercell, if you want to differentiate between atoms in "different unit cells".

Yes, of course, you can change color and transparency level of the color in VESTA software. You can follow following question:

https://www.researchgate.net/post/Crystal_Structure_in_Vesta

Dinesh Kumar

I cannot see that the link you provide is helpful concerning the specific question asked above.

I think you can use Xcrysden you can change the color

http://www.xcrysden.org/

Andreas and Lee,

The given link is working properly as I checked ever if not, then follow the following steps for changing the color of polyhedra:

Draw ball and stick model ------> in style tab select "polyhedral" -----> go to objects tab -------> select polyhedra -----> click on the color in front of element say Zn (A) below column C -------> choose desire color and click "OK" --------> You get the change in color

You can also see in the attachment.

Dinesh Kumar It appears to me that you modify the colour of all polyhedra associated with a certain crystallographic site are modified. The question had referred to change the colour of a specific out of several crystallographically equivalent polyhedra. So it is no solution of the problem.

Dear Andreas Leineweber and Hyungjun Lee ,

In the VESTA software one can change color of the equivalent polyhedra in the crystal structure. Further, on can keep different colors for equivalent polyhedra of different crystallographic sites (see attachment). One can not change color of single polyhedron of the same equivalent polyhedra among the numbers of polyhedra.

[The above molecular structure is for ZnO which has only one type of polyhedra i.e. tetrahedra. Color changes for all polyhedra associated with the same equivalent polyhedra.]

Dinesh Kumar If you would have read the previous answers, you would know how it works to change specic polyhedra. This is what all this is about.

Ok, Thanks.