NIH 3D Workflows
NIH 3D provides automated workflows to convert scientific data formats into 3D mesh files. Supported workflows process both mesh-based and data-based inputs and output standard 3D file formats suitable for visualization and 3D printing. Additional formats and features are in development.
Terminology
Mesh File
A 3d object composed of vertices, edges, and polygons (e.g., .glb, .stl, .x3d, .wrl)
Data File
Scientific datasets (e.g., .cif, .pdb, .sdf, DICOM) used to generate mesh files via visualization tools
Quick Submit
An automated workflow that uses a database identifier to fetch molecular structure data and generate 3D mesh files without manual uploads, enabling rapid model creation
Workflow Categories
NIH uses VTK and SimpleITK to convert a .zip of CT-based .dcm files into a 3D mesh. The workflow:
- Applies a bone-threshold filter
- Extracts the largest connected mesh
- Discards noise or improperly structured files
Expected input structure:
dicoms.zip/├── image01.dcm├── image02.dcm└── ...Only properly formatted CT image series are supported. For unsupported formats, consider 3D Slicer or Horos
Accepted formats: .glb, .x3d, .stl, .wrl
Note:
- .stl files do not support vertex colors
- Uploaded .glb files with textures/animations are preserved but may render in greyscale due to our rendering pipeline (this will be addressed in our upcoming Workflows 2.0 release)
Uses Blender to repair models for 3D printing:
- Fixes non-manifold edges and intersections
- Merges overlapping components
- Repaired files are suffixed with _mr
Note: Not all inputs are repairable. STL outputs from ChimeraX workflows are repaired by default.
Quick submit auto-generates models and fetches metadata from known scientific databases using UCSF ChimeraX and the NIH Presets found in the ChimeraX Toolshed. Users cannot edit these entries, but may contact us with concerns.
Supported sources:
- AlphaFold (alphafold.ebi.ac.uk)
- Submit with UniProt ID (e.g., Q8W3K0)
- Outputs include "all" (entire structure) and "hc" (high-confidence regions, pLDDT > 50).
- Additional styles:
- pLDDT-mapped coloring
- Domain coloring via Predicted Alignment Error (PAE)
- PDB (rcsb.org)
- Submit 4-character PDB (e.g., 6VXX)
- Obsolete IDs are rejected; download .cif for manual upload instead
- PubChem (pubchem.ncbi.nlm.nih.gov)
- Use the Compound CID (numeric ID). A 3D structure must be available.
- EMD (EMDataResource)
- Submit numeric portion of the EMD accession (e.g., 10499 from EMD-10499)
UCSF ChimeraX and the NIH Presets, NIH 3D can process:
- .cif, .pdb, .sdf, .mol, mol2, .map, .omap, .mae, .pdb1, .ent, .tiff, and .tif
Processing steps:
- Classification: Auto-detected as small molecule, medium, or large macromolecule
- Bond inference: Based on interatomic distances for <30 atom structures
- Symmetry expansion: For user-supplied files with symmetry data
- Volume rendering: Automatic contouring using 1% voxel density or EMDB suggestion
- Output: .glb (with vertex color), .stl, .x3d, .wrl. Only monochrome outputs are converted to .stl.
Outputs from Molecular/Quick Submit Workflows
Summary:
- Codes ending with -print indicate versions intended for 3D printing with thickened ribbons or surfaces and structural support features.
- Codes ending with -vis are for visualization only and do not include printing adaptations.
- Prefixes like all- indicate full AlphaFold models, while hc- denotes high-confidence filtered regions based on pLDDT > 50.
- Ribbon codes relate to backbone representations colored by secondary structure, chain, rainbow, or AlphaFold confidence metrics.
- Surface codes relate to molecular surfaces colored by chain, hydrophobicity, electrostatics, or AlphaFold confidence metrics.
Software References
Blender
Blender Foundation. (2002-present). Blender [Computer software]. https://www.blender.org
ChimeraX
Meng, E. C., Goddard, T. D., Pettersen, E. F., Couch, G. S., Pearson, Z. J., Morris, J. H., & Ferrin, T. E. (2023). UCSF ChimeraX: Tools for structure building and analysis. Protein Science, 32(11), e4792. https://www.cgl.ucsf.edu/chimerax/
Pettersen, E. F., Goddard, T. D., Huang, C. C., Meng, E. C., Couch, G. S., Croll, T. I., Morris, J. H., & Ferrin, T. E. (2021). UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Science, 30(1), 70-82.
Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018). UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Science, 27(1), 14-25.
Note: ChimeraX is developed by the Resource for Biocomputing, Visualization, and Informatics at UCSF with support from NIH R01-GM129325 and the NIAID Office of Cyber Infrastructure and Computational Biology.
PyMesh Lab
Muntoni, A., & Cignoni, P. (2021, January). PyMeshLab [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.4438750
SimpleITK
Beare, R., Lowekamp, B. C., & Yaniv, Z. (2018). Image segmentation, registration and characterization in R with SimpleITK. Journal of Statistical Software, 86(8). https://doi.org/10.18637/jss.v086.i08
Yaniv, Z., Lowekamp, B. C., Johnson, H. J., & Beare, R. (2018). SimpleITK Image-Analysis Notebooks: A collaborative environment for education and reproducible research. Journal of Digital Imaging, 31(3), 290-303. https://doi.org/10.1007/s10278-017-0037-8
Lowekamp, B. C., Chen, D. T., Ibáñez, L., & Blezek, D. (2013). The design of SimpleITK. Frontiers in Neuroinformatics, 7, 45. https://doi.org/10.3389/fninf.2013.00045
Trimesh
Dawson-Haggerty, D., & contributors. (2013-present). Trimesh: A Python library for loading and using triangular meshes [Computer software]. https://github.com/mikedh/trimesh
VTK (The Visualization Toolkit)
Schroeder, W., Martin, K., & Lorensen, B. (2006). The Visualization Toolkit: An object-oriented approach to 3D graphics (4th ed.). Kitware, Inc.
Kitware, Inc. (2000-present). The Visualization Toolkit (VTK) [Computer software]. Retrieved June 3, 2025, from https://vtk.org