User:Marius Mihasan/Sandbox 1

From Proteopedia

Jump to: navigation, search

Contents

Proteopedia and 3D Printing

Physical molecular models, by engaging both visual and tactile senses, provide an effective means of deepening the understanding of complex concepts in molecular biology and biochemistry. They allow students to perceive the three-dimensional organization of macromolecules, thereby enhancing comprehension of the relationship between structure and function [1] [2]. Numerous studies have demonstrated that the use of tangible models in science education improves learning outcomes, fosters conceptual reasoning, and increases student engagement [3] [4] [5]. The rapid development of 3D-printing technologies has made it possible to create customized and affordable molecular models [6] [7] [8].

Affordable desktop 3D printers can now be used to fabricate physical models from virtually any scene on Proteopedia. This page provides an introduction to 3D printing, a step-by-step guide to generating printable files directly from Proteopedia, and several tested printing profiles for common printers (e.g., Prusa Research, Bambu Lab, Creality, or Elegoo).

Let’s 3D-print the whole Proteopedia!

Introduction to 3D printing / 3D Printing 101

about printers (FDM vs SLA) single vs multimaterial and files Understanding printer types, materials, and file formats

Explain the main 3D printing technologies used for molecular models: FDM (Fused Deposition Modeling) – affordable, suitable for large colorful models, layer-based printing. SLA/DLP (Resin Printing) – higher resolution, suitable for small detailed models. Note differences between single-material vs multi-material printers. Introduce file formats commonly used in Proteopedia and 3DP-Jmol workflows: .STL (geometry-only) .OBJ (geometry + color/texture) .3MF (newer format, supports multi-material and color metadata). Provide one or two illustrative photos of printed examples or link to downloadable models.

Overview of the 3D printing process

the path from structure/scene to physical object - including slicers and profiles From molecular structure to physical object Stepwise diagram (PDB → Jmol Scene → 3DP-Jmol export → STL/3MF → slicer → printer). Briefly explain what slicers are (PrusaSlicer, Bambu Studio, Cura, Chitubox, etc.). Emphasize the role of profiles (printer settings: layer height, infill, temperature, supports). Optional: add a short embedded animation showing a molecule being “sliced” layer by layer.

Generating printable files on Proteopedia

how to use the tool with screenshots, or maybe better, a movie? Step-by-step illustrated guide (with screenshots or a short video): Open any Proteopedia page and load a scene. Activate the Print3D tool (mention integration link). Choose representation type (cartoon, spacefill, surface, etc.). Adjust scale and export to STL/3MF. Notes on scaling limits, coloring, and how to combine multiple chains or ligands.

If possible, embed a short instructional video (1–2 min) —

Printing

This is where we provide printing profiles and instructions From file to physical model Provide tested printing profiles (e.g., downloadable .ini or .3mf files) for common printers: Prusa Research (MK3S, MK4, Mini) Bambu Lab (P1P, X1C) Creality (Ender 3, K1) Elegoo (Mars, Saturn – for resin printing). Include detailed settings for successful printing (layer height, infill %, speed, supports, post-processing).

Add example photos of successful prints from Proteopedia scenes (credit your lab or collaborators). Optionally: subsection on painting and finishing models for color or texture enhancement. - i do not do it, its not required. Maybe a link?

Other relevant resources

Curated list of external links: Tutorials (e.g., NIH 3D Print Exchange. GitHub repository of 3DP-Jmol (link to documentation and issue tracker). Proteopedia help pages for embedding 3D-printable content. List of major printing services provider - maybe a link on Gmaps that would search for 3D printing services in the user region?

If you print a model from Proteopedia, please share photos and feedback — let’s 3D print the whole Proteopedia!

References

  1. ↑ Howell ME, Booth CS, Sikich SM, Helikar T, van Dijk K, Roston RL, Couch BA. Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships. Biochem Mol Biol Educ. 2020 Jul;48(4):356-368. PMID:32590880 doi:10.1002/bmb.21362
  2. ↑ Răzvan-Ştefan B, Laura Nicoleta P, Mihășan M. Impact of 3D-printed molecular models on student understanding of macromolecular structures: a compensatory research study. Biochem Mol Biol Educ. 2025 Jul-Aug;53(4):358-369. PMID:40214166 doi:10.1002/bmb.21902
  3. ↑ Smith DP. Active learning in the lecture theatre using 3D printed objects. F1000Res. 2016 Jan 13;5:61. PMID:27366318 doi:10.12688/f1000research.7632.2
  4. ↑ Srivastava A. Building mental models by dissecting physical models. Biochem Mol Biol Educ. 2016 Jan-Feb;44(1):7-11. PMID:26712513 doi:10.1002/bmb.20921
  5. ↑ Larsson, C., Tibell, L.A.E. Challenging Students’ Intuitions—the Influence of a Tangible Model of Virus Assembly on Students’ Conceptual Reasoning About the Process of Self-Assembly. Res Sci Educ 45, 663–690 (2015). DOI: 110.1007/s11165-014-9446-6
  6. ↑ Da Veiga Beltrame E, Tyrwhitt-Drake J, Roy I, Shalaby R, Suckale J, Pomeranz Krummel D. 3D Printing of Biomolecular Models for Research and Pedagogy. J Vis Exp. 2017 Mar 13;(121):55427. PMID:28362403 doi:10.3791/55427
  7. ↑ Mihasan M. A beginner's guideline for low-cost 3D printing of macromolecules usable for teaching and demonstration. Biochem Mol Biol Educ. 2021 Jul;49(4):521-528. PMID:33755300 doi:10.1002/bmb.21493
  8. ↑ Segarra VA, Chi RJ. Combining 3D-Printed Models and Open Source Molecular Modeling of p53 To Engage Students with Concepts in Cell Biology. J Microbiol Biol Educ. 2020 Dec 21;21(3):21.3.72. PMID:33384761 doi:10.1128/jmbe.v21i3.2161

Proteopedia Page Contributors and Editors (what is this?)

Marius Mihasan

Retrieved from "http://52.214.119.220/wiki/index.php/User:Marius_Mihasan/Sandbox_1"
Personal tools