Show clip caps on atoms and ribbons

[Tom Goddard]

Zheng Ruan asked about showing clip caps on ribbon helix tubes.

Currently we don't cap these because the appearance is bad due to limitation of our clip cap code.

Begin forwarded message:

From: Zheng Ruan via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] Filled helix tube when clipped
Date: May 27, 2022 at 1:49:15 PM PDT
To: ChimeraX Users Help <chimerax-users@…>
Reply-To: Zheng Ruan

Dear ChimeraX users,

I'm curious to know if there is a way to have the helix tube filled
when after using the clip command? I know that the clip plane of
surface representation can achieve this as found in this example
(https://www.rbvi.ucsf.edu/chimerax/feature_highlights/pmc.png).
However, I'm not able to make it when I display my structure in
cartoon cylinder representation. I attached an example image that I
made.

Thank you for your input.

Best,
Zheng

[Tom Goddard]

I tried enabling caps for atoms and ribbons and made some images. The appearance is bad with missing caps and wrong color caps and cap edge distracting lines. It would be hard to fix these problems so I don't expect we will ever be able to support this.

One basic problem is that the clip cap code can only compute the cap when the clip plane intersected with the surface makes a closed loop boundary. If the surface being clipped has an edge and the plane intersects the edge then there is no closed loop and there is no cap shown. Many surface boundaries are hidden. For instance in a ribbon between every 2 consecutive residues there is a hidden boundary. In other words, each individual residue of the ribbon is its own surface patch disconnected from (but coincident with) its neighbors. So clipping ribbons only shows a cap about half the time.

A second problem is that instanced objects like the atom spheres of a structure only make a single cap, not a separate cap for each sphere and the single cap has one color. So for multiple atom colors, the cap ends up not matching the atom colors.

These problems are illustrated in some images I have attached.

[Tom Goddard]

Clipped atom spheres, single color.

[Tom Goddard]

Clipped atom spheres, multiple colors.

[Tom Goddard]

Clipped ribbon with tube helices, no caps due to cylinder seams.