Dear ChimeraX users,

I am reaching out for assistance with visualizing amino acid residues in ChimeraX, particularly when part of the residue is embedded within a cartoon structure representation. 

I am aiming to achieve a visualization similar to what is possible in PyMOL, where the complete residue is visible even when it intersects with other structural elements and adjust the transparency of the cartoon representation so that the embedded atoms of the residue can be clearly seen. I am struggling to get the desired result.

To provide context and illustrate the issue, I am enclosing images of the current visualization:

• Image 1: Shows the current state where part of the residue is obscured by the cartoon structure.
• Image 2: Demonstrates the desired outcome where the residue is fully visible, including the embedded atoms.

I am looking for a solution that combines the aspects seen in the two attached images, allowing for clear visualization of the residue and improved transparency.

Thank you very much for your assistance. I look forward to your guidance on how to achieve this in ChimeraX.

Best regards,

Amandeep

--

Amandeep Sharma

PhD Student (2024-25)

Dept. of Bioscience & Bioengineering

Indian Institute of Technology Jodhpur

Karwar 342037, Rajasthan

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