ChimeraX Recipes

These are examples of ChimeraX command use and Python scripts to perform various tasks.

Command Examples

• Realign a map so symmetry axis is along z. May 22, 2023
• Show a transparent surface with shadows. February 10, 2023
• Record a microscopy movie with a time label. October 21, 2022
• Measure a virus interior volume. November 3, 2021
• Record a movie flipping through electron microscopy planes. April 22, 2021
• Depict monomer rotation in a dimer. December 18, 2020
• Make a helical filament atomic model. September 10, 2020
• Color a sliced surface by B-factor. September 9, 2020
• Show surface exposed hydrophobic residues. September 7, 2020

Python Examples

• Copy coordinates between conformers. February 24, 2023
• Rotate a density map 90 degrees about z axis. January 25, 2023
• Move a surface to highest intensity in 3D microscope image. December 1, 2022
• Inspect atomic data structues interactively in Python. November 23, 2022
• Show colored axes and coverslip for 3D image data and a timestamp label. October 20, 2022
• Show convex hull for a set of atoms. October 10, 2022
• Animate a phage tail helix contracting. September 11, 2022
• Lookup residues by chain identifer and residue number. August 2, 2022
• Color a surface using vertex values from a file. July 27, 2022
• Set camera view to match PyMol. June 24, 2022
• Place linkers with molecular dynamics. March 18, 2022
• Add bonds between close atoms. March 16, 2022
• Select overlapped atoms. March 16, 2022
• Copy chain colors from one structure to another. January 14, 2022
• Make ViewDockX table information available as model attributes. December 17, 2021
• Compute variance of a series of maps. November 24, 2021
• Label secondary structure elements. November 8, 2021
• Find closest pair of atoms. September 28, 2021
• Open multi-segment AlphaFold structures. September 8, 2021
• Save multiple fits of a structure in a map. July 26, 2021
• Complete side chains of an atomic model. June 10, 2021
• Select atoms in a map subregion. May 21, 2021
• Read an MRC file and write a subregion. May 21, 2021
• Show ellipsoid for diffusion tensor depiction. March 16, 2021
• Show atoms from Gaussian cube files. February 2, 2021
• Read CASTP pockets files. January 18, 2021
• Save images of each chain of a structure. December 11, 2020
• Display square mesh grid. October 19, 2020
• Place markers on connected surface pieces. October 8, 2020
• Speed comparison with Biopython. September 15, 2020
• Change atom z coordinates z -> -z. September 3, 2020
• Create spherical harmonic surface. August 28, 2020

C++ Examples

• Running C++ computations in a separate thread. October 1, 2020