Hi Reza, There are several commands and tools that calculate atom-atom interactions and draw dotted lines. See menu: Select... Contacts (choose "Atomic"). This uses the Contacts tool, which you can also start directly from the tools menu (Tools... Structure Analysis... Contacts). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> There is also Tools... Structure Analysis... H-Bonds. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> These are also available as commands: contacts, clashes, hbonds <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> You may want to take a look at the Protein-Ligand Binding Sites tutorial which covers some of these features: <https://rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> If you mean you want to choose 2 atoms manually and draw a dotted line, just add a distance measurement. Ctrl-click one atom, Shift-Ctrl-doubleclick second atom, choose distance from pop-up menu, see selection context menus: <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context> ... or, you can use the distance command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> However, if you meant you want a 2D graph (not in the 3D window), sorry there is no 2D diagram of atomic interactions currently. 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 Oct 12, 2024, at 9:29 AM, Reza Khayat via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I'm hoping this question wasn't asked before. Is there a way to draw a dotted line between interacting residues? This would be similar to the Chain Interface graph that shows interaction between chains. Thanks.

Best wishes, Reza

Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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