What version of ChimeraX are you using? Also, for the problematic pseudobond are either of its endpoint atoms not peptide backbone atoms? If so, you will have to explicitly display the non-backbone atom in order for the pseudobond to show (display of backbone atoms is "implied" by the cartoon depiction). Alternatively, you could delete the non-backbone atoms of the endpoint residue.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Feb 4, 2022, at 9:19 AM, Wout Oosterheert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX team,

I’m making figures of a protein structure that has 4 residues missing in a flexible region. When I show the atoms as “style stick”, I can see a dashed pseudo bond between the two residues that connect the missing segment. However, when I “show cartoons” of the same structure, the dashed line disappears and the pseudo bond is no longer visible. Would you have any suggestions on what to change to make the missing structure appear as a dashed line when the model is shown in cartoon style?

Of interest, in a similar structure where 3 instead of 4 residues are missing, the dashed line is in fact shown when the model is shown in cartoon style. In addition, in regular Chimera the dashed line that represents the 4 missing residues remains visible in cartoon style.

Thank you for your time.

Best wishes,
Wout

Wout Oosterheert, PhD
Max Planck Institute of Molecular Physiology
Otto-Hahn-Str. 11
44227 Dortmund, Germany
Phone +49-(0)231-133-2357
Email: wout.oosterheert@mpi-dortmund.mpg.de

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