Export and import¶
Each plot tab provides an Export menu for the displayed figure and the data used to draw it. Export the CSV together with a publication figure so processing and units remain inspectable.
Figures are written directly as EPS. JPEG export uses Ghostscript or ImageMagick when available and otherwise falls back to EPS; check the status message and resulting extension.
Plot exports¶
| Tab | Principal CSV content |
|---|---|
| Pore Profile | channel coordinate, radius, and selected fill property where applicable |
| Over Time | frame-by-position radius or property matrix |
| Mean Profile | coordinate, mean radius, standard deviation, and contributing-frame count |
| Trends | frame and selected metric |
| Histogram (radius summary) | axial-bin coordinate and uncapped mean/minimum/maximum radius aggregate |
| Hydration | coordinate, relative density, free energy, waters per frame, and available standard deviations |
| Ion Flow | plotted occupancy or passage data and species metadata |
Additional exports include summary metrics, bottleneck residues, unrolled pore-wall layers, and tunnel lining data. Inspect the CSV header: it is the authoritative statement of columns and units for that export.
Connolly openings¶
With Color set to pore_lobes, each region gear exports the pore or one
lateral opening. The header gear exports all regions. The all-frame table
includes occurrence, dot count, neck, extension, axial position, and azimuth.
An opening absent from a frame has present=0 and blank measurement cells.
Filenames¶
VMDHole suggests a descriptive filename for each export. Confirm the destination before saving.
Hydration export¶
Hydration CSV export always writes the mean density/free-energy profile, independent of the currently displayed hydration view. Per-frame matrix and hydrophobicity plot names must not be interpreted as extra columns in that profile file.
Tunnel lining¶
In tunnel mode, Lining → Export writes lining data for the selected route. Standard plot exports remain CSV.
Saved runs and import¶
When Save results is enabled, each frame has a result directory and the run root contains provenance/manifest data. Use File → Import to restore a saved HOLE or tunnel calculation without executing the engine again. Imported data can be plotted and exported, but analyses that need the original trajectory coordinates, such as ion tracking, also require the matching molecule and frames to be loaded in VMD.