User Guide¶

This guide matches the gatewizard-gui desktop app (Electron). The gatewizard pip package is the Python API only — it does not open this window.

Pages¶

The left activity bar switches pages:

Visualize workspace

Visualization¶

1. Open a PDB/mmCIF (or paste an RCSB id).
2. Use the toolbar: Open / Select / Tools / Save Image.
3. Representations dock: cartoon, licorice, surface, coloring, selections.
4. Orbit with the left mouse button; Ctrl+scroll zooms more slowly.

Trajectories¶

Load a topology + DCD/XTC/TRR (or PSF+DCD). The play slider and optional Traj-smooth cards appear once frames are available.

Animation¶

Turn Animate on for a keyframe timeline. Export GIF/WebM/PNG (transparent background is available for those formats; MP4/MOV stay opaque).

Tools on Visualize¶

Tools ▾ includes mutate residue, split chain, superimpose, and related edits. Mutate writes a new structure into the session.

Save Image opens the figure dialog (size, scale, transparent PNG, yellow crop overlay).

Preparation¶

PropKa table plus an inline 3D view of the working PDB.

1. Set the working directory (top bar) and load a PDB.
2. Choose pH and optional protein capping (ACE/NME).
3. Run analysis. The table lists residue, Old ID, New ID, chain, pKa, and state at pH.
4. Auto-detect disulfide bonds if needed, then Prepare (missing protein heavy atoms from Amber templates, PropKa names, AmberTools hydrogens). Missing loop residues are not built. Stale CONECT/LINK records are dropped. If the Amber reduce binary is missing, Prepare keeps tleap hydrogens and still writes a prepared PDB.

Keep original residue numbers and chains is on by default. PropKa and AmberTools still add hydrogens; residue and chain ids stay as in the input (a missing loop that jumps from 200 to 205 stays that gap). Uncheck it for sequential Amber numbering (tleap / MD).

Capping is for fragments and termini that should not stay charged in MD. The capper still writes ACE as residue 1 and shifts the chain for its own file; Prepare with preserve on puts the protein numbers back. New ACE/NME then get N-terminus − 1 (residue 0 if the chain starts at 1) and C-terminus + 1. The capper mapping file is kept for later Builder/PropKa steps.

Builder¶

Leaflet composition, water/ions, and parametrization. Each run is a job card under the project folder.

1. Working file: prepared protein (or uncheck protein for bilayer-only and set membrane XY).
2. Upper/lower lipids and ratios. GateWizard supports 4028 lipids from the packmol-memgen catalog (--available_lipids_all, version 2025.1.29). Each row shows the residue name, charge, and chemical name. The catalog lists 4055 names; the 27 SIRAH lipids are coarse-grained and are not supported. A short familiar subset is in the builder reference.

1. Water model, protein FF, lipid FF, salt, water thickness.
2. Validate, then generate inputs / start preparation. Watch the job card; Cancel stops a running run_preparation.sh.

Keep Skip protonation on when the PDB already has PropKa names (ASH, GLH, HIP, CYX).

Equilibration¶

Pick an engine (NAMD, GROMACS, OpenMM, Amber), a scheme (NVT/NPT/…), then Generate.

Jobs¶

Progress cards: Watch (local logs), Pull (sync from a remote job), and per-stage status.

Cluster¶

Run on cluster uses Settings → Clusters (SSH, workdir, Slurm). The dialog writes a cluster run script next to the local equilibration folder.

Tools¶

Fix PBC unwraps/centers a trajectory for analysis or Visualize. Other tools on this page stay job-based (status JSON in the project folder).

Folder-wide job scans pause while you are on Visualize so playback stays smooth.

Analysis¶

Two modes on the same page:

• Structural — RMSD, RMSF, distances, Rg, area-per-lipid / thickness (FATSLiM, GridMAT, or lipyphilic).
• Energetic — NAMD / OpenMM / GROMACS / Amber log plots. Engine selector chooses the parser.

Selections use MDAnalysis syntax (protein and name CA). Multi-file runs need per-file times so the x-axis is in ns, not concatenated steps. Details: Analysis features.

Settings and clusters¶

Gear → Clusters: host, user, key, remote workdir, optional scratch. GPU safe mode is session-only unless you change it here.

Status bar¶

The footer shows backend connectivity and system RAM (not polled while you stay on Visualize).

Python API¶

For scripts, use the API reference and method dictionary. Worked examples are the tests/<module>_examples/ scripts in the API repository.