Drawing Crystal Structures

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Crystal structures of refined phases can easily be drawn as ball-and-stick or polyhedral graphs with the software Vesta. This tutorial shows how to export the data from Profex and how to import it to Vesta. The project „Olivine Quartz“ from the BGMN example library is used for demonstration. The files can be downloaded here:

Linux and OS X: OlivineQuartz-unix.zip
Windows: OlivineQuartz-windows.zip

Vesta is freely available for Windows, OS X, and Linux:
http://jp-minerals.org/vesta/en/download.html

Exporting structure data to CIF

Run Profex and open the file olivinequartz.dia from the example project. Run the refinement:

fig1-project

When the refinement has terminated, select „Results -> Export CIF files from LST files…“ to export the refined structure data to CIF files:

fig2-export-Cif

In the following dialog you can choose the projects from which you want to export the data. Make sure the project „olivinequartz“ is selected and click „OK“.

fig3-select-project

Profex will export the data and print the location of the new CIF files to the refinement protocol console:

fig4-cif-output

Structure drawing with Vesta

Now run Vesta and select „File -> Open…“. Set the file format to „Crystallographic Information File (*.cif; *.mcif)“, and open the exported file „olivinquartz-FORSTERITE.cif“:

fig5-vesta-open

The structure will be drawn with spheres representing the atoms:

fig6-vesta-struc

Fine tuning the drawing

Go to „Edit -> Bonds…“ to define polyhedra. In the following dialog click „New“ (1), select „Si“ for the first atom (2), and „O“ for the second atom (3), and enter a maximum bond length of 1.7 (4). Then click „OK“:

fig7-vesta-bond

Now all SiO4 groups will be drawn as ball-and-stick groups. Set the style to „Polyhedral“ to draw SiO4 tetrahedra:

fig8-vesta-poly

Select „Objects -> Boundary…“ and set x(min), y(min), and z(min) to -0.5, and x(max), y(max), z(max) to 1.5 in order to show a larger section of the structure.

fig9-vesta-boundary

Select „Objects -> Properties -> Polyhedra“ to change the representation of the tetrahedra if desired. Then save and/or export the file:

fig10-vesta-exported


Nicola Doebelin, January 2016