3DP-Jmol
Accessible 3D-printed molecular models for everyone
Accessible 3D-printed molecular models for everyone
is a simple tool that automatically generates 3D printable molecular models from structural data.
Have you ever wanted/needed a model of a particular macromolecule to improve your teaching or your (thesis) presentation? Or to help you better understand the structure of complex biological (macro)molecules? The available models are limited or too expensive? Then you need to 3D print your own (macro)molecular model.
A vast body of literature indicates the using physical molecular models during teaching and learning significantly increases the learning outcomes by offering a tangible way to view and manipulate physical structures in three dimensions and by challenging students to engage with and interrogate the model. Nowadays, the amount of data deposited in structural databases such as wwPDB or PubChem is so large, that practically any molecules found in text-books is available. Combined with the recent developments in 3D-Printing technologies, this offers a unique opportunity – any lesson in bio-molecular sciences can be turned into a physical molecular scene that students can interact with.
The most user-intensive step in generating 3D printable models of macromolecular structures is the conversion of the structural data into the stl file. This step is key not only for the printability of the model but also for its success as an educational or demonstration material. Important key information related to the target molecule such as size, atoms, and bond dimensions must be correlated with the final dimensions of the physical model and printing hardware. Hence we started developing 3DP-Jmol – a tool that automatically generates 3D printable molecular models from structural data based on very minimal user input.
3DP-Jmol is distributed under a MIT License. Please visit the 3DP-Jmol Github for its source code and for more technical details.
3DP-Jmol was jointly developed by Dr. Marius Mihasan, Biology Department, Alexandru Ioan Cuza University of Iasi, Carol I Bvd., No.11, 700506, Iaşi, Romania and
Dr. Angel Herráez, Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá, E-28805 Alcalá de Henares (Madrid), Spain. Testing and web-implementation is supported by EDUMOL3D, Project PN-IV-P7-7.1-PED-2024-0343 financed by the Ministry of Research, Innovation and Digitization, UEFISCDI, Romania.
Locate your structure of choice and identify its PDBID: a 4-letter code that should look like this: 4hhb. For teaching and learning purposes, we highly recommend looking on PDB101 and Proteopedia for inspiration. For advanced users with knowledge in structural biology, we recommend RCSB PDB.
For now, running the script is only possible by using the command line. Please fallow the instructions available here. We are working on making the tool available in a web page and integrate it with Proteopedia.
A successful run of the script will generate .stl file that can be 3D printed. Either upload them to your favourite printing service, or open them in your preferred slicer. Print them and enjoy.
