Parameter reference

This page lists VMDHole controls and their starting values. Saved settings can change a default.

Shared input

Parameter	Default	Definition
Molecule	top	VMD molecule to analyse
Selection	protein	Atoms that define the pore or molecular interior
Frames	now	now, all, one frame, start:end, or start:stride:end
Align trajectory	off in pore mode; on for tunnel tracking	RMSD-fit frames to a reference selection before analysis
Alignment selection	protein and name CA	Atoms used for the fit
Reference frame	0	Frame used as alignment reference

Pore geometry

Parameter	Default	Definition
CPOINT	VMD centre of rotation	Initial point inside the pore, in Å
CVECT	{0 0 1}	Direction of the channel axis
Stabilize CPOINT	off	Carry the point with a local rigid-body fit in every frame
Local fit radius	10 Å	Initial neighbourhood for CPOINT or endpoint stabilization
Auto-expand fit radius	15 Å	Larger neighbourhood used if the initial fit has too few atoms
Fit RMSD warning	3 Å	Console-warning threshold for an unstable local fit
Track CPOINT	off	Re-centre the point on selected atoms near its previous position
Track radius	8 Å	Neighbourhood used by CPOINT tracking
Stabilize CVECT endpoints	off	Carry each two-point endpoint with an independent local fit
Exact CVECT selection	off	Re-evaluate both point selections in every frame; mutually exclusive with endpoint stabilization
Show cues	off	Mark CPOINT, CVECT, or the tunnel start in the VMD viewer
Radius file	configured HOLE file	HOLE .rad file containing van der Waals radii for every selected atom
SAMPLE	0.25 Å	Distance between successive search planes
ENDRAD	15 Å	Radius at which HOLE considers an end open to bulk
SHORTO	1	HOLE output verbosity; 1 suppresses detailed per-slice diagnostics while retaining the profile output
IGNORE	HOH WAT TIP SOL	Residue names excluded from the HOLE calculation
Random seed	blank (uses 1)	Integer seed; blank uses 1

Radius files

The radius file assigns a van der Waals radius to every selected atom. Choose a HOLE-format .rad file in File → Settings and confirm that the console reports no missing atom types. Use a custom file for cofactors, ligands, modified residues, or nonstandard naming.

Atomic radii are separate from the bare, hydrated, and probe radii used by Passability. Their sources are listed in References.

HOLE method and search

Parameter	Default	Definition
Method	Spherical	Spherical probe, Connolly accessible cross-section, or Capsule anisotropic probe
Search	Monte Carlo (HOLE)	HOLE's seeded simulated annealing, or the deterministic Nelder-Mead search in nm_search. The Monte Carlo rows apply only to Monte Carlo; Capsule always uses HOLE. Both stop the profile at ENDRAD, so their Volume readouts agree
Dot density (Settings, shown for sos_triangle)	15	sph_process dots per sphere; not used by the marching-cubes mesher
Monte Carlo steps	blank (HOLE default 1000)	Optimization steps per search plane
Monte Carlo step size	blank (HOLE default 0.1 Å)	Trial displacement scale
Monte Carlo temperature	blank (HOLE default 0.1)	Simulated-annealing acceptance parameter
Connolly surface (HOLE parameters, Connolly runs only)	HOLE conn	Under a Monte Carlo search, HOLE's conn or the nm_search port of it (same algorithm, byte-identical dots on the same centres). Nelder-Mead always uses the port
Surface mesher (Settings → Engines, first row)	Marching cubes, grid 1.4 Å / neck 0.7 Å	Meshes the spherical, Connolly and tunnel surfaces with mesh_csg: marching cubes on the exact sphere union, with the edge crossings solved against the sphere itself rather than interpolated. One mesh serves both playback and the settled view, so the surface never changes shape when playback stops. The default matches sos_triangle's triangle size at dot density 15; lower grid for a finer surface at more cost per frame. A Connolly run uses grid uniformly, because its whole surface is at probe scale and has no narrow neck to refine. The grid and neck entries appear only for the marching-cubes mesher. sos_triangle is the alternative; Capsule always uses HOLE. Property colouring recolours whichever mesh is current, and the marching-cubes one has no polygon limit, which is what let a dense Connolly run colour at all
Hide sideways spill	off	Remove Connolly surface regions classified as lateral spill
Margin	2 Å	Distance beyond the traced pore wall that still belongs to the central pore
Opening axial match tolerance	6 Å	Maximum axial displacement used to match a lateral opening across frames
Opening angular match tolerance	35°	Maximum azimuthal displacement used to match a lateral opening across frames
Opening Seen floor	25%	Minimum percentage of analysed frames required to list a tracked opening
Extra cards	blank	Additional HOLE control cards, separated by semicolons

Tunnel search

Parameter	Default	Definition
Start point	blank	Buried origin coordinate; may be derived from a selection's centre of geometry (COG) or VMD's centre of rotation (COR)
Auto-detect origins	off	Detect candidate internal cavities rather than use only the entered point
Probe	3.0 Å	Probe used in accessible-space construction
Interior threshold	1.25 Å	Minimum clearance used to classify interior voids
Origin radius	5.0 Å	Radius around the requested start used to accept seeds
Minimum length	0 Å	Minimum accepted route length
Bottleneck	1.25 Å	Minimum accepted bottleneck radius
Minimum depth	8 Å	Required graph depth of an interior seed
Minimum depth length	5 Å	Minimum length associated with the depth criterion
Surface cover radius	10 Å	Surface neighbourhood used in terminal classification
Auto-origin cover radius	10 Å	Cover radius used during automatic-origin selection
Maximum origins	5	Maximum automatically selected origins
Bottleneck tolerance	0 Å	Tolerance applied to the bottleneck filter
Maximum similarity	0.9	MOLE similarity threshold for redundant routes
Weight function	VoronoiScale	Route cost: VoronoiScale, LengthAndRadius, Length, or Constant
FBL	off	Enable the MOLE FBL option
Strict Interior	off	Apply a stricter interior classification; may yield no routes for borderline inputs

Tunnel exits and clustering

Parameter	Default	Definition
Custom exit point	blank	User-defined surface target
Custom path start/end	blank	Directed path constraint
Use custom exits only	off	Exclude automatically found exits
Cluster within frame	on	Merge similar routes in one frame
Within-frame cutoff	3 Å	Distance threshold for within-frame route clustering
Cross-frame maximum deviation	12 Å	Largest geometric deviation accepted as one tracked route
Ranks per frame	10	Highest-ranked routes admitted to cross-frame matching; 0 means all
Seen floor	40%	Minimum frame occupancy shown for a tracked route
Align trajectory	on	Fit frames before route matching
Pre-mesh budget	400	Limit for eagerly prepared route meshes
Draft detail	1	Tunnel surface sampling stride
Tunnel dot density	15	Surface sampling density
Accurate 3D coloring	off	Project a tunnel property by true 3D surface distance

Visualization and property controls

Parameter	Default	Definition
Pore representation	Isosurface	None, Centerline, Dots, Wireframe, or Isosurface
Tunnel representation	Isosurface	Isosurface, Wireframe, or Centerline; global or per route
Pore surface color	hole_def	HOLE radius banding, property, pore_lat pore/spill classification, pore_lobes individual Connolly openings, or a flat VMD color
Tunnel surface color	automatic rank	Route/rank color, selected property, or a flat VMD color
Material	Opaque	VMD material applied to the generated representation
Playback stride (Settings, sos_triangle mesher only)	4	Draw every Nth triangle while the trajectory plays; the marching-cubes mesher always draws full detail
Synchronize playback	on	Update VMDHole geometry with the VMD frame
Pore lining threshold	3 Å	Maximum atom-to-local-surface distance used to classify lining residues for display and residue-property averaging
Property smoothing	3 Å	Axial smoothing bandwidth
Pore-facing only	on	Retain side chains directed toward the lumen where applicable
Accurate 3D property projection	on	Project property to the true surface rather than a faster approximation
Bottleneck shell	3 Å	Independent surface-distance cutoff for the bottleneck-residue report
Scale bar	on/default	Show property legend in the VMD scene
Scale-bar font/corner	saved/default	Legend color and screen position
Metrics readout	on/default	Show pore summary and selected ion passability values
Metrics species	Water, K, Na, Ca	Species in the on-figure passability summary; Mg, Cl, Li, and Cs are also available

The 3D surface, Pore Profile Fill, and Mean Profile synchronize a property where it is available. Over Time has an independent property and an explicit Compute gate. Kapcha–Rossky is atom-level in both modes.

Plot controls

Tab	Controls
Pore Profile	None, Fill, Ellipse fit, or Unrolled; property/layer; ellipse solid/point rendering; swap axes; flip direction
Over Time	Radius or Property; HOLE or Ellipse radius source; color scheme; independent property; Compute; flip Y
Mean Profile	2D fill; property; 3D isosurface; color; material; accurate 3D; frame cap; Render smoothly (off); swap/flip
Trends	metric; mean overlay; conductivity preset/custom value for conductance; constriction shell
Histogram (radius summary)	mean (default), minimum, or maximum radius over 50 fixed spatial bins; swap/flip

See Properties for Unrolled layers. Connolly reach is available for Connolly pores. Plot swap and flip options change presentation only. The unrolled map requires a native HOLE binary.

Hydration

Parameter	Default	Definition
Water selection	water and oxygen	One representative oxygen atom per water molecule
Temperature	310 K	Temperature in -RT ln(rho/rho_bulk)
Bin width	1 Å	Axial density-bin width
Density probe cap	configured/default	Maximum radial region used for density; 0 uses the full pore radius
Density probe floor	0 Å	Minimum probe radius; 0 disables it
Bulk density	measured; fallback 0.0334 Å⁻³	Reference density, displayed read-only
Gaussian KDE	on	Smooth axial water density
KDE bandwidth	1.4 Å	Smoothing bandwidth; auto fits each frame and matches CHAP's software default
Poisson energy floor	on	Apply a finite sampling-limited barrier to empty bins
Zero energy at mouths	on	Shift the mean mouth free energy to zero
CHAP mode	off	Apply CHAP-compatible defaults
Fix leucine hydrophobicity	off in CHAP mode	Use corrected leucine value rather than exact CHAP-table compatibility

Available views are Density, Energy, Hydrophobicity, and Per-frame ρ. Hydration is pore-only and requires explicit water.

Reporting a free-energy barrier

Bandwidth controls how strongly the water profile is smoothed and can change a narrow barrier's height. Use auto when matching CHAP's software defaults. Use a fixed bandwidth when consistent spatial resolution across frames or systems is required. Compare more than one bandwidth when the conclusion depends on a narrow gate, and always report the selected value. A floor-limited dry-bin barrier is a sampling-dependent lower bound.

Ion Flow, permeation, and passability

Parameter	Default	Definition
Ion Flow view	Occupancy %	Occupancy map, Passage tracks (water crossings coloured by direction), or Count vs frame (one curve per ion type when all are selected)
Passage Show (Water only)	All crossing	All crossing, Passage up, Passage down, or All entered (adds the molecules that never crossed)
Species	All detected	All = every ion type, never water; Water = one oxygen per molecule from the Hydration water selection
Shell	3 Å	Radial region beyond the mean pore wall included in the map
Stride	1	Trajectory sampling stride for ion analysis
Flip Z	off	Reverse plotted pore direction
Permeation bulk planes	automatic	Two bulk boundaries along the per-frame pore axis
Time between saved frames	blank	Required to convert counts to rates
Applied voltage	blank	Required, with time, to estimate conductance from net transferred charge
Passability salt	150 mM NaCl at 37 °C	Bulk-conductivity preset used by geometric conductance readout
Passability custom conductivity	1.9 S/m	Used when Custom is selected
Water probe radius	1.15 Å	Probe radius used in accessible-volume/passability metrics
Readout species	Water, K, Na, Ca	Species shown in the on-figure summary

Ion Passage means an ion entered the near-pore region. Permeation requires a complete crossing from one bulk region to the other. Bare/hydrated passability is a steric comparison, not a free-energy calculation.

Files and performance

Parameter	Default	Definition
Output directory	automatic	Root for persistent frame directories and manifest
Save results	on	Keep results instead of using temporary storage
Overwrite	on	Replace prior stored frames after GUI confirmation
Keep visualization	on	Retain generated VMD molecules/representations
Keep input PDB	off	Preserve exact per-frame coordinates submitted to an engine
Prebuild surfaces	off	Generate surfaces before they are displayed
Parallel jobs	automatic	Normally available cores minus one
Surface cache	20 frames	Number of prepared surfaces retained in memory
Mean-profile frame cap	1000	Maximum frames used for expensive mean 3D/property work; 0 uses all frames

Configure executable paths and the radius file in File → Settings. See Installation for recommended binaries.

Minimum reporting set

For a reproducible pore analysis, report the structure/trajectory, frame range and time stride, periodic imaging and alignment, atom selection, radius file, CPOINT, CVECT, method, SAMPLE, ENDRAD, seed policy, and software/binary versions. Add dot density and Monte Carlo parameters when changed.

For tunnel analysis, also report origin selection, probe/interior/bottleneck thresholds, weight function, exit constraints, within-frame clustering, cross-frame matching parameters, and the Seen threshold. For hydration or ion analyses, report selections, temperature, density reference, binning and smoothing, trajectory time spacing, bulk planes, voltage, and PBC treatment as applicable.