Issue with Display of Hydrogen Bonds in Find H Bond Tool in Chimera
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 -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=publicacao_visualizar&id_documento=1160855&id_orgao_publicacao=0>
Hi Gabriele, The Find H Bond tool only finds H-bonds. Sometimes if your structure does not have the hydrogens, however, it will draw the line between two heavy (nonhydrogen) atoms. This does not mean that the tool detected a polar interaction that is not an H-bond. Instead it just means that it detected an H-bond from the possible positions of the inferred virtual hydrogens (imagined possible possible positions of the hydrogens based on the chemical types of the heavy atoms) even though your structure did not have these hydrogens explicitly. From the FindHBond help page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html> "The H-bonds will be shown as lines (a group of pseudobonds named hydrogen bonds) between the donor and acceptor atoms, or if hydrogens are present, between the hydrogens and acceptor atoms." That means that you can add all the hydrogens (e.g. command "addh" or AddH tool) before using Find H Bond and then you will only get lines that are between the H atom and the H-bond acceptor. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2024, at 3:02 PM, GABRIELE SANTOS CEPINHO via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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
participants (2)
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Elaine Meng -
GABRIELE SANTOS CEPINHO