Dear Chimera Support Team,

My name is Gabriele Cepinho, and I am using Chimera version 1.17.3 for molecular docking analysis in my research. Recently, I encountered an issue with the Find H Bond tool that I have been unable to resolve, and I hope you may be able to assist me.

When I use the Find H Bond tool to display hydrogen bonds between molecules, the generated image also shows polar interactions along with the specific hydrogen bonds. However, in the tool’s output file, I can clearly identify which interactions are true hydrogen bonds.

My goal is to display only the hydrogen bonds in the image, excluding the polar interactions, but I have not been able to adjust the tool to achieve this. I have tried modifying the distance and angle parameters to restrict the display, yet polar interactions still appear alongside the hydrogen bonds in the visualization.

I appreciate any guidance or recommendations you can provide regarding this matter. If there is any additional option to filter these interactions directly in the image, or if there is an update or specific setting available for the Find H Bond tool, I would be grateful to know about it.

Thank you in advance for your attention.

Best regards,

Gabriele Cepinho