The most straightforward way to write to a file that can only hold a single frame is to use the write() method of any AtomGroup. MDAnalysis uses the file extension to determine the output file format. For instance, to only write out the Cα
𝐶
𝛼
atoms to a file in GRO format:

ca = u.select_atoms('name CA')
ca.write('calphas.gro')
Trajectories
The standard way to write out trajectories is to:

Open a trajectory Writer and specify how many atoms a frame will contain

Iterate through the trajectory and write coordinates frame-by-frame with Writer.write()

If you do not use the context manager and the with statement below, you then need to close the trajectory with .close().

For instance, to write out the Cα
𝐶
𝛼
atoms to a trajectory in the XTC format:

ca = u.select_atoms('name CA')
with mda.Writer('calphas.xtc', ca.n_atoms) as w:
for ts in u.trajectory:
w.write(ca)
Analysis
MDAnalysis comes with a diverse set of analysis modules, and the building blocks to implement your own. (Please see a list of analysis tutorials in the user guide.)

The majority of these follow a common interface:

Initialise the analysis with a Universe and other required parameters.

Run th