If I understand correctly, you want it to look something like this? If so, the command you want is "cartoon suppressBackboneDisplay false". Best, Tristan [image: image.png] On Mon, Aug 19, 2024 at 4:38 PM Amandeep Sharma (P24BB0001) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Dear Elaine and Tristan, Thank you both so much for your prompt and detailed responses! I really appreciate the clear instructions and examples you've provided. Tristan, the "cartoon suppress false" command worked perfectly for my needs. Elaine, your additional guidance on selectively showing and hiding backbone atoms, along with adjusting ribbon transparency, was exactly what I was looking for. Thanks again for your help and for pointing me in the right direction. Best regards, Amandeep On Mon, Aug 19, 2024 at 9:47 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Thanks Tristan!

Amandeep, what he said is exactly right, if the goal is to allow showing backbone atoms at the same time as the ribbon. After turning off "suppressBackboneDisplay", you can then show and hide whichever backbone atoms that you want -- you don't have to show them all. Making the ribbon transparent is a separate, independent step.

Example commands:

open 1gcn show :10-14 transparency 50 target c cartoon suppress false

See help for "cartoon" and its options including "suppressBackboneDisplay": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>

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 Aug 19, 2024, at 8:44 AM, Tristan Croll via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

If I understand correctly, you want it to look something like this? If so, the command you want is "cartoon suppressBackboneDisplay false".

Best, Tristan

...

On Mon, Aug 19, 2024 at 4:38 PM Amandeep Sharma (P24BB0001) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: 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