These are examples of ChimeraX command use and Python scripts to perform various tasks.
Command Examples
- Show CAVER biomolecular channels and tunnels. October 3, 2023
- Aliases for atomic model building as done in Coot from Oliver Clarke. September 6, 2023
- 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
- Measure spots seen in 3D microscopy. November 6, 2023
- Set atom size proportional to bfactor. July 24, 2023
- Run Python code when mouse hovers over atom. July 6, 2023
- 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