Hi David, Our expert(s) on this topic are away currently, but may be able to give you a better answer later. (A) If you mean that that you want to cut open the surface and see inside (as opposed to drawing a planar cap so that the surface would still be enclosed), one concern is that this surface is very thin and may not be useful for 3D printing. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcapper/surfcapper.html> (B) I don't know what format you are using to export the surface, but nearly all of these formats have the limitation that they do not include clipping, see Limitations: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> I know that STL format is sometimes used for 3D printing, but as mentioned in the above, STL export does not include clipping. The X3D format is documented to include per-model clipping but not global clipping. However, you may not be able to use this format for 3D printing anyway. Per-model clipping vs. global clipping and how to do either one: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html> (C) Since this is volume data (a density map) maybe it could be done by limiting the extents of map display by methods other than clipping, such as: - showing only a subregion (however, this would still be a rectangular box aligned along map X,Y,Z axes) <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions> - Volume Eraser (however, it may be difficult to erase exactly what you want to erase) or "vop" options that erase octants <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> - masking to a surface (however, I tried clipping the isosurface and masking the map to its own clipped isosurface, but that procedure also ignores clipping). It can, however, give a thick "shell" around the isosurface which might be more suitable than the isosurface itself for 3D printing, if there is some way to actually cut that shell open along the clipping plane. This type of shell can be produced with "mask" options "sandwich false" and "slab N" where N is the thickness of the slab in distance units. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> Maybe others will be able to advise how/whether what you want can be done in Chimeral, or whether you would have to postprocess the mesh in some other application. Sorry I couldn't be more helpful, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 22, 2022, at 12:35 PM, Haselbach,David via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi,

I wanted to build a cut open model of a cryoEM map which I achieved through clipping in Chimera. But I am failing to apply the clipping in a way that I can save the cut open mesh as poligone file for 3D printing. Is this possible?

All the best,

David