Hi Jana,

Elaine is right. The clip planes are just a graphics operation that hides parts of your molecular surface in front of some plane. The actual surface is not changed, and the STL output contains the actual models, not the graphical depiction of the models.

ChimeraX does not have a way to create a cut solvent-excluded molecular surface. There are tricks to cut a Gaussian surface, you can create a surface with the molmap command, e.g. "molmap protein 2.5" but this kind of surface looks a lot different and is probably not what you want. You use volume cropping to cut it. That has the extra complexity that the volume can only be cropped along x,y,z axes, so to get the cut plane oriented the way you want requires additional trickery to reorient the axes of the volume. I don't recommend this route. But I don't have a better solution available right now.

I have some code from our old program Chimera, its "sop clip" command that would actually cut a surface to a sphere rather than a plane. But the same code can easily cut using a plane. It is not in ChimeraX. I would be interested in adding it to ChimeraX for cutting with a plane, maybe I can look next week. Been on a work trip all this week and may be busy next week trying to catch up, so not sure if I will have time.

Tom

On Feb 23, 2024, at 3:16 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Dear Jana, Probably the limitations for exporting the scene in STL are the same in ChimeraX as in the documentation for Chimera, namely

"Only what is displayed will be exported. Note that something can be displayed yet invisible due to clipping or zoning, or because it simply falls outside the current view."

https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html

...i.e. clipping or zoning does not really remove the parts from the model, it just makes them invisible, but as you reported, they will still be included in the exported file.

I need to doublecheck with the other developers that this applies to ChimeraX similarly as in Chimera before I update the ChimeraX documentation, but I believe that is the issue.

I don't know of a workaround. Sorry about that. Elaine

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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On Feb 23, 2024, at 2:38 PM, Jana Villemain via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Greetings,

I have downloaded the attached .pdb. Also attached is a screenshot of same model, but sliced specifically at histidine 65. I need to export the edited file, sliced, as an .stl so that I can print it. However, try as I might, every time I save, or export the file, it is unedited – and includes the entire model. Any help you could provide would be great!

<image001.png>

Thank you,

Jana

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