Hi Vincent, This is a well-known problem with 3D printing models that contain intersecting surfaces. The ChimeraX bonds and atoms are intersecting cylinders and spheres. The 3D printer software takes your STL and makes "tool paths" saying where to extrude plastic, and it often makes hollow regions when two surface intersect. Here's an example to understand this better. Suppose you have two concentric sphere surfaces one smaller than the other that defines a spherical shell. The two spheres don't intersect. 3D printer software will fill the region between the two spherical surfaces to make the shell and won't fill the inner sphere with plastic -- it will be hollow. Now suppose the inner sphere is moved so that it intersects the outer sphere. That is like the situation in ChimeraX if you show atoms as spheres. You probably want the 3D printer software to fill both spheres with plastic. But in fact, most software will leave the intersection of the interior of the two spheres empty. Basically if a point is inside two (or any even number of surfaces) then the 3D printer software often leaves it emtpy, not filling with plastic. At any rate, it may be that your 3D printer software has an option for "mesh intersection logic" which lets you say fill all intersecting surfaces. In the past that was not available and processing molecular models for 3D printing involved a step to eliminate the mesh intersections. The NIH 3D web site fixes the STL files by building a new mesh without the intersections. They used to do that with a program called MeshLab. Here is the NIH 3D site, and maybe just submitting your model to NIH 3D would help you get a printable file. https://3d.nih.gov/ Tom

On Jun 25, 2026, at 8:14 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

a little off-topic question, but not completely...

a standard conversion of .pdb to .stl works very well and 3D prints perfectly.

I encounter a problem with the addition of pbonds as in the attached image. converting an atom in a sphere of larger diameter is fine (top image). But adding a pbond from the center of that sphere results in empty spaces created at the intersection between objects (bottom image, 2 white arrows). There is also no real cohesion between the 2 objects (left arrow), which results in a very weak printing.

Any ideas on how to make the 2 object fuse entirely?

Thank you. Vincent

-- Vincent Chaptal, PhD CNRS research director Team leader Drug Resistance and Membrane Proteins Lab

MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 https://mmsb.cnrs.fr/en/team/drug-resistance-and-membrane-proteins-drmp/

_______________________________________________

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