I guess you are using the "surface dust" command or Hide Dust tool in ChimeraX to hide small surface blobs. Then when you export as GLTF it includes the displayed triangles. Each triangle is defined by three indices into an array of vertices. That array of vertices includes all the hidden blob vertices too, which is I think what you are observing. ChimeraX does not get rid of the vertices that are part of the hidden blobs, because they are merely hidden and you may want to redisplay them. ChimeraX also does not currently have a way of deleting the hidden blobs.

I don't know how you are analyzing the GLTF, but if you write your own code to do it then you could take just the vertex indices that appear in the GLTF array of triangles. If this is too difficult I could give you some Python code so ChimeraX could delete the hidden vertices and hidden triangles.

On Oct 6, 2021, at 10:18 AM, Scott, Brandon L. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I'm having an issue with gltf exporting with hidden objects. The surface that is exported looks correct; however, when querying the points in the exported file all the hidden ones are there as well which is hindering a downstream analysis.

Exported gltf:

Rendered points from gltf:

Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor
Nanoscience & Nanoengineering
South Dakota Mines
501 E. Saint Joseph St., Rapid City, SD 57701
724.510.1253 | Brandon.Scott@sdsmt.edu
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