Properties and color scales

Property maps add physicochemical context to a geometric pore or tunnel. They do not convert a radius profile into a permeability calculation. Report the scale, lining definition, smoothing, and analysis mode with any property-colored figure.

Available properties

Interface label	Quantity and source	Important restriction
Kyte–Doolittle	Residue hydropathy	Residue-level average
Wimley–White (interface)	Interfacial hydrophobicity	Residue-level average; CHAP uses its own compatible variant
Kapcha–Rossky	Atomic hydrophobicity assignment	Tunnel mode uses atoms in the tunnel lining
Fauchère–Pliska	Residue lipophilicity	Distinct from MOLE logP
Formal charge	Assigned residue formal charge	Not a pH-dependent electrostatics calculation
Grantham polarity	Residue polarity	Sequential scale
MOLE hydropathy, hydrophobicity, polarity, charge	MOLE lining-property tables	Distinct from similarly named pore scales
MOLE logP, logD, logS	MOLE residue lookup values	Do not substitute one for another
MOLE mutability	MOLE residue mutability lookup	Higher values indicate the table's variable end
MOLE ionizable	Count/indicator from MOLE residue assignments	Not a protonation-state calculation
Electrostatic potential	Relative potential in kcal mol⁻¹ e⁻¹	Requires appropriate charge data
Water G(z)	Water free energy derived from density	Requires Hydration Compute
Water density	Water depletion field	Requires Hydration Compute

Tunnel mode offers Kyte–Doolittle, Wimley–White, Kapcha–Rossky, Fauchère–Pliska, and the MOLE properties in the table. Electrostatic potential and hydration-derived properties are pore-only.

Non-protein residues in the selection

The residue-level scales (Kyte–Doolittle, Wimley–White, Fauchère–Pliska, Grantham polarity, and the MOLE tables) are amino-acid tables. A selected residue that is not in them — a glycan, lipid, ligand, or cap — takes a neutral placeholder value and is announced once per residue name in the console; no published value exists for such residues on these scales, so their colour is a placeholder, not a measurement.

Two schemes remain fully meaningful for heteroatoms: Kapcha–Rossky is atom-level — with partial charges loaded (PSF/topology) it applies the original |q| < 0.25 e rule to every atom directly, glycans included — and the water schemes (G(z), density) are computed from the water itself. Prefer those, or plain radius, when a glycan or lipid lines the region of interest. Formal charge is also correct for neutral sugars (zero).

The full numerical ranges and primary references are listed in References. Nonstandard residues absent from the MOLE lookup table receive a neutral fallback and generate a warning; assign their chemistry outside the plugin or interpret the aggregate cautiously.

How a slice receives a value

For residue properties, VMDHole identifies lining residues within the selected surface-distance shell, optionally applies the pore-facing filter, assigns each residue its table value, and smooths the result along the route. Pore and tunnel lining definitions differ, so aggregate values should not be compared across modes as if they were generated from the same samples.

Two independent distance controls have the same default:

• Pore lining threshold (default 3 Å) classifies lining residues for the lining/facing displays and residue-property averaging.
• Bottleneck shell (default 3 Å) selects residues for the constriction report.

Changing one does not change the other.

Where properties appear

The 3D surface, Pore Profile Fill, and Mean Profile synchronize a selected property where that property is available. Over Time has its own selector and Compute step.

After Hydration has been computed, Pore Profile Fill and Mean Profile offer trajectory-average Water G(z) and Water density. The 3D surface instead offers current-frame Water density when per-frame hydration data exist.

Unrolled map layers

Unrolled maps use wall distance, oxygen/nitrogen identity, residue number, chain (or segment), and polarity. They also offer Kyte–Doolittle, Wimley–White, Fauchère–Pliska, formal charge, Grantham polarity, MOLE logP, logD, logS, mutability, and ionizable assignment. Polarity is its own wall classification, not formal charge.

After a Connolly run, Connolly reach reports the maximum radial extent of the Connolly surface in each axial and angular map cell. Large patches identify lateral expansions that can be examined as individual openings with the pore_lobes surface color. This differs from Wall distance, which reports the nearest pore-wall atom along a ray from the axis.

Reading colors

Read the legend, not color alone: its range stays fixed across frames. For a signed property, the middle is zero; other properties run from low to high. Water density is shown as depletion, 1 - ρ/ρ_bulk: positive values are below bulk density and negative values are above it.