Module 4: Molecule Viewer

Tutorial – Module 4

Module 4 – Molecule Viewer

LUMPAC 2.0 introduces a new molecule viewer module (Figure 1) for observing, editing, and saving images of the studied complex structures and calculated molecular orbitals.
Figure 1. Module responsible for the molecule visualization.
1. Click on button (Figure 2) to open the desired input file.
After opening the desired file, the structure will be displayed, as in Module 1 (Figure 11).
Figure 2. LUMPAC interface for opening the input file for structural visualization of the complex.
2. To visualize the orbitals of the complex, select the options on the right side of the screen (Figure 3).
LUMPAC 2.0 requires the utility orca_plot.exe program to visualize molecular orbitals (Figure 3). This program is distributed with ORCA and is in the same directory as orca.exe. The orca_plot.exe program creates .cube files for the selected orbitals, which will be saved in the directory containing the files with orbital information (.gbw, .nto, or .loc) created during the excited states calculations. Figure 3 illustrates how to select molecular orbitals for visualization.
Figure 3. Interface with options for generating molecular orbitals.
3. Select the orbitals for rendering, following the instructions in Figure 4.
Figure 4. Interface for selecting the molecular orbitals to be rendered.
4. Once rendered, the orbitals will be displayed superimposed on the molecule (Figure 5).
Figure 5. Visualization of the rendered molecular orbital in the molecule viewer.
LUMPAC 2.0 includes a feature called “Join Images” (Figure 5) for organizing and labeling the molecular orbitals into a single image, and the available options are displayed in Figure 6. The individual orbital images are saved as .png format, while the combined image is saved as new_image.jpg.
Figure 6. “Join Images” window with options for combining the orbital images.