How to measure and visualize the distance between two benzene rings in ChimeraX?
Dear ChimeraX Developers, I am working with a protein-ligand complex where there seems to be a π-stacking interaction. I would like to measure the distance between the benzene ring of an amino acid residue in the protein and the benzene ring of the small molecule ligand. Could you please advise on the specific steps within ChimeraX to perform this measurement and also visualize it (e.g., showing the distance label)? Looking forward to your answer, thank you! Best regards, Nan Nan Zhang zhangnan@nankai.edu.cn
Based on your next question, I guess you figured it out! Define centroids of rings and then measure distance between them, as detailed in the other messages. Regards, Elaine
On Jun 11, 2025, at 7:23 AM, Nan Zhang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Developers, I am working with a protein-ligand complex where there seems to be a π-stacking interaction. I would like to measure the distance between the benzene ring of an amino acid residue in the protein and the benzene ring of the small molecule ligand. Could you please advise on the specific steps within ChimeraX to perform this measurement and also visualize it (e.g., showing the distance label)? Looking forward to your answer, thank you! Best regards, Nan
Nan Zhang zhangnan@nankai.edu.cn
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participants (2)
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Elaine Meng -
Nan Zhang