Visualization

VMDHole creates separate VMD molecules or representations for calculated geometry. These objects are visual aids tied to numerical results; they do not modify the analysed structure.

Pore representations

Mode	Content	Use
None	No generated geometry	Batch analysis or fastest plotting
Centerline	HOLE sphere centres	Verify the path and endpoints
Dots	Surface sample points	Inspect sampling and difficult geometry
Wireframe	Mesh edges	Inspect topology without an opaque surface
Isosurface	Triangulated pore surface	Presentation and property mapping
Ellipse surface or point cloud	Fitted non-circular cross-sections	Inspect slit-like pore shape

To display the ellipse, choose Ellipse fit in Pore Profile, then choose Solid surface or Point cloud from Render. It is available for Spherical pore analyses, not Connolly or Capsule analyses.

Start with Centerline. Interpret profiles or physicochemical maps only after the path is shown to occupy the intended pore in representative frames.

Connolly and high-density surfaces can exceed the stock HOLE surface converter's limits. Use the accelerated sos_triangle, reduce dot density, or use Centerline when the mesh is not needed.

Tunnel representations

Tunnel routes support Isosurface, Wireframe, and Centerline views. Use the global gear to set defaults and a row gear to override one route. Per-route controls include visibility, color, property color, material, and representation. Show all applies to routes that pass the current tracking and Seen filters.

Color and properties

A pore surface can retain HOLE's radius bands, use a flat VMD color, or use a supported physicochemical or hydration property. In Connolly mode, pore_lat distinguishes the central pore from lateral extensions. Select pore_lobes to open the inline region table, where each tracked opening can be shown, colored, annotated, and exported independently. See Connolly lateral openings for the measurements in that table. A tunnel can use automatic route/rank color, a flat color, or a property. Fixed property-scale limits keep the same meaning across frames and figures. See Properties for data sources and restrictions.

The main surface, Pore Profile Fill, and Mean Profile synchronize a property where it is available. Over Time is independent and recalculates only after Compute.

Lining and pore-facing residues

Lining creates VMD selections for residues close to the pore or tunnel surface. The distance is measured from molecular surface to calculated surface, not from an atom centre to the centreline.

Pore-facing only further restricts eligible side chains to those directed toward the lumen. This filter does not apply to atom-level Kapcha–Rossky values or water-derived fields.

Playback and caching

With synchronization enabled, moving the VMD frame slider selects the corresponding calculated frame. Surface meshes are built lazily and held in an in-memory cache. Relevant controls are:

• Prebuild surfaces: prepare all selected frames before playback.
• Surface cache: retain a limited number of meshes.
• Playback stride (Settings, sos_triangle mesher only): draw every Nth triangle while the trajectory plays.
• Keep visualization: retain generated VMD objects after a run or reset.

Prebuilding improves interactive playback but increases initial runtime and disk use. A larger cache reduces rebuilding but increases memory use.

Mean 3D surface

Mean Profile can revolve the mean radius profile into a trajectory-average 3D surface. It is not an average Cartesian molecular surface. Property color can be projected with the fast approximation or Accurate 3D mode. Render smoothly applies mesh smoothing to this mean surface and is off by default; record both choices when comparing figures.

Scale bar and metrics

The 3D scale bar reports the selected property and its fixed range. Its corner and font color are presentation settings. The optional metrics readout shows radius, volume, conductance estimates, and selected steric passability values. Those annotations do not alter exported numerical data.