What should I do to visualize the Mayer bond orders (calculated by using AOMix-L) in UCSF Chimera?
• Start UCSF Chimera on your computer. • In the Chimera menu: go to File and then Open, then select the XYZ file (or any other Chimera-readable structure file) for your molecule. Press the Open button at the bottom of the Open-File-in-Chimera window. You should see the structure of your molecule in the Chimera screen. • In the Chimera menu: go to Tools and then Depiction and then PseudoBond Reader. Select the AOMix-L-atom-chimera2.txt file and press the Open button at the bottom of the Open-File-in-Chimera window. You should see the Mayer bond orders (the default color is blue) for all the bonds that have calculated bond orders greater than the threshold value (0.1). You can edit the AOMix-L-atom-chimera2.txt file before importing its data to Chimera to suit your needs: • you can remove bond order data for atomic pairs that are not useful for your presentation; • you can change the bond order depiction color; • you can change the number of significant figures for the bond order (the de
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