Hi Samo, That bond isn’t because of the distance, it’s because it’s indicated in the input file you are using — either the topology file if its a trajectory, or by the CONECT records of a PDB file (or the equivalent for mmCIF). It wouldn’t be hard to post process the structure to remove those bonds. I’ll open a ticket for that so you’ll be notified when it gets implemented. In the interim, it is really easy to remove those bonds. Just use the command “~bond H”. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 27, 2026, at 4:27 AM, Samo Lešnik via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers,
I have a small suggestion: if the residue name is detected as HOH, TIP3, WAT, ... (whatever the list of waters are), then the bond between H2 and H1 is not drawn, as this is an artifact of the small distance.
Best regards,
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