Code


Search for or select a topic from the pull down menu to find scripts, code and programs created by NIAID researchers related to computational biology and bioinformatics. Have some code to share? Send us an email here. Are you aware of the NIAID GitHub site?

Blender_PNG_from_X3D.py


Imports a monochrome .x3d model into Blender and automatically generates a snapshot in .png format and exports a model in .stl format.

Blender_STL_Cleanup.py


Imports a .wrl file into Blender, cleans the mesh, and exports .stl, .x3d, and .blend formats.

Blender_VRML_cleanup_ribbon.py


Imports a .wrl model into Blender and cleans the mesh; exports a .x3d scene, and a model in .blend format. This script is used with molecular ribbon models generated in Chimera, using Chimera_Molecular.py

Blender_Blend_from_X3D Set.py


Imports a generic .x3d into Blender and exports it in .blend format.

Blender_STL_to_X3D.py


Imports a .stl model into Blender, recolors it, and exports in .x3d and .blend formats.

Blender_VRML_Cleanup.py


Imports a .wrl model into Blender and cleans the mesh; exports a .x3d scene, and a model in .blend format. This script is used with molecular surface models generated in Chimera, using Chimera_Molecular.py

Chimera_Volumetric.py


Using UCSF Chimera, generates isosurface meshes from volumetric data (e.g., microscopy image stacks). Outputs monochrome surface as .stl, and radial-colored surface as .wrl.

Chimera_Chem.py


Using UCSF Chimera, generate color and monochrome versions of a small molecule in ball-and-stick, CPK, and stick variations. Models are optimized for 3D printing and exported as .wrl and .stl files.

Chimera_Molecular.py


Using UCSF Chimera, generate several color and monochrome models from molecular data in variations of ribbon and surface structure. Models are optimized for 3D printing and exported as an .x3d scene.

cor_to_pdb.f90


Reads a CHARMM formatted coordinate file and write a PDB formatted coordinate file.

pdb_to_charmm.f90


Reads a PDB file in RCSB or VMD format and writes CHARMM formatted sequence and extended coordinate files.

splitpdb1.sh


Splits a multi-molecular PDB file into individual files.

PrimerID pipeline


Processes data produced using the PrimerID method for amplicon sequencing to generate viral population frequency tables for nucleotides and amino acids.