I have the file in Pymol for example or as a PDB image . Can someone provide a guideline how this can be converted for 3D printing ? Thanks in advance
Hi Ivan,
I learnt that this was quite difficult using Pymol, however, using Chimera (I use version 1.14) this task became rather simple!
Hope this will help you.
Best of luck!
Hello Ivan,
I can only fully agree with the suggestion Samuel Sellberg made. We use the same process and are pretty happy with it.
Best regards
Guido
Dear Ivan Kadurin
1. open your PDB file in the chimera
2. Change the representation as per your need
3. go to file-export scene
4. change file type STL or OBJ for 3D printing
Hello Ivan,
PyMOL can directly export PDB into 3D printing file by File-Export Image As, you can save as a .wrl or a .stl file.
PyMol can give great models for 3D printing. Simply increase the quality of the representations, for example by tweaking sphere_quality, cartoon_oval_quality, stick_quality, surface_quality, and so on. If you don't change these settings, the standard representations optimised for screen viewings will not be watertight, and will lead to prints containing visible holes. After optimising these settings, select "Export Image As", "STL"
Here are some settings that worked for me:
# generally I don't print hydrogens and solvent molecules
hide everything
remove hydrogens
remove solvent
# sphere settings
show spheres, SELN # replace SELN with your chosen selection name or "all"
set sphere_scale, 0.7, (all)
# set spheres to render triangles, so that viewing represents the exported file
set sphere_mode, 0
set sphere_quality, 3
# cartoon settings
show cartoon, SELN
set cartoon_oval_width, 0.7
set cartoon_sampling, 10
set cartoon_oval_quality, 20
# licorice settings
show licorice, SELN
set stick_radius, 1
set stick_ball, 1
set stick_quality, 20
# surface settings
show surface, SELN
set surface_quality, 1
set solvent_radius, 0.5
you can use chimera ucsf to produce the x3d file then use https://imagetostl.com/convert/file/x3d/to/obj
to convert it into object
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