Quickstart¶

This quickstart is intentionally practical. It is not the full workflow, but it gets you from a trajectory or cluster folder to the relevant applications.

The command examples below assume the package is installed in your active environment. If you are launching directly from a source checkout, use the PYTHONPATH=src conda run --no-capture-output -n saxshell-py312 python -m ... pattern from Installation. For example, saxshell saxs ui maps to python -m saxshell.saxs ui.

1. Inspect and export frames¶

If you are starting from a trajectory:

mdtrajectory inspect traj.xyz --energy-file traj.ener
mdtrajectory export traj.xyz --energy-file traj.ener --use-suggested-cutoff --temp-target-k 300 --window 3

This gives you a folder of exported frames that can feed the next stage.

2. Optional XYZ to PDB conversion¶

If you need residue-aware PDB frames before clustering:

xyz2pdb preview splitxyz --config residue_map.json
xyz2pdb export splitxyz --config residue_map.json

Skip this stage if plain XYZ cluster extraction is enough for your system.

3. Extract clusters¶

Launch the cluster UI:

clusters

Or inspect a frame folder from the terminal:

clusters inspect splitxyz

4. Analyze bond and angle distributions¶

bondanalysis inspect clusters_splitxyz0001
bondanalysis run clusters_splitxyz0001

5. Launch the SAXS workflow¶

Open the SAXS UI:

saxshell saxs ui

Inside the UI, the normal path is:

Create or open a SAXS project.
Point the project at your experimental data and cluster folder.
Build the SAXS components in Project Setup.
Review the model in SAXS Prefit.
Run SAXS DREAM Fit if you need Bayesian refinement.

6. If you are starting from an existing project¶

You can open a project directly:

saxshell saxs ui /path/to/project

The same pattern also exists for the fullrmc UI:

saxshell fullrmc ui /path/to/project

Next step¶

Go to Project Setup for the first SAXS-specific workflow in the GUI.