Visualization has always been a crucial part of the educational process. Implementing computer algorithms and virtual reality tools into it is vital for the new generation engineers, scientists and researchers. In the field of chemistry education, various software that allow dynamic molecular building and viewing are currently available. These software are now used to enhance the learning process and ensure better understanding of the chemical processes from the visual perspective. The present short communication provides a summary of these applications based on the NarupaXR program, which is a great educational tool that combines the functionality and simple design necessary for an educational tool. NarupaXR is used with a companion application “Narupa Builder'' which requires a different file format, therefore a converter that allows a simple transition between the two extensions has been developed. The converter sufficiently increases the efficiency of the educational process. The automatic converter is freely available on GitLab (https://gitlab.com/teamSCAMT/converter_mol2_to_xml). The current communication provides detailed written instructions that can simplify the installation process of the converter and facilitate the use of both the software and the hardware of the VR set.