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Pore tutorial: gramicidin A

This case study develops a reproducible pore analysis of PDB 1GRM. Its purpose is to establish the workflow: define the system, verify the pore geometry, analyse an ensemble, and record enough information to repeat the calculation.

Objective

Measure the gramicidin channel radius in each NMR model and compare the profiles. The structure contains five models and no explicit water, ions, or membrane. Hydration, ion-flow, and permeation analyses therefore do not apply.

1. Load and inspect

Load vmdhole/1GRM.pdb. Display all atoms and confirm that the two peptide chains form one continuous channel. Select all in VMDHole because the terminal groups are not included by VMD's protein macro.

2. Define an axis independent of file orientation

Use the terminal groups at opposite channel mouths:

  1. Select ⌖ beside CVECT.
  2. Set point 1 to resname ETA and chain A.
  3. Set point 2 to resname ETA and chain B.
  4. Select Compute and inspect the displayed vector; the stick above it can then tilt the direction by whole degrees if needed.
  5. Set CPOINT to the centre of geometry of all.

This definition remains meaningful if the coordinates are rotated. If the profile is displayed in the opposite direction from the desired convention, reverse the two points or use the plot flip control.

3. Run one model and validate the path

Set Frames to now, keep the spherical method, and select Run HOLE. Switch the 3D representation to Centerline and check that:

  • the path lies inside the channel;
  • both ends reach bulk-facing openings;
  • the path does not jump into an external groove;
  • the narrow region is consistent with the molecular structure.

If any check fails, do not tune the plot. Correct the selection, CPOINT, or CVECT and rerun.

4. Make the run reproducible

Open HOLE parameters and confirm the random seed. A blank value resolves to the fixed seed 1; enter another integer only when the protocol requires it. Record:

  • structure identifier and model or frame range;
  • VMD atom selection;
  • radius file;
  • CPOINT, CVECT, SAMPLE, ENDRAD, and SHORTO;
  • pore method and dot density;
  • Monte Carlo seed, steps, step size, and temperature;
  • VMDHole, HOLE, and binary versions.

HOLE uses stochastic optimization. Exact reruns and method comparisons require the same effective seed and otherwise identical inputs.

5. Analyse the five-model ensemble

Set Frames to all and rerun. For comparisons across a genuine trajectory, first make the protein whole, image it consistently, and align it to a reference selection. The five 1GRM models are already suitable for this small example.

Use the analysis tabs in this order:

  1. Pore Profile: inspect individual frames and locate the constriction.
  2. Over Time: confirm that the same axial region is compared across frames.
  3. Mean Profile: report mean radius and variation along the pore.
  4. Trends: compare minimum radius or pore volume per model.
  5. Histogram: examine the distribution without implying a time sequence.

Ellipse-based quantities require an additional cross-section calculation. The Over Time tab displays a Compute gate before this expensive calculation; select it deliberately and retain the source label in exported results.

6. Add physicochemical context

Select a residue property such as Kyte–Doolittle or Wimley–White. The 3D surface, Pore Profile fill, and Mean Profile property share one selector. Over Time has an independent property selector and requires Compute after a property or cutoff change.

Use Pore-facing only when the question concerns the physicochemical environment presented to the lumen. Report the property scale, surface-distance cutoff, and smoothing bandwidth.

7. Export

Export the Pore Profile figure and CSV, Mean Profile CSV, and Trends CSV. Keep the run directory or manifest with the analysis. A figure without its parameter set, radius file, frame definition, and trajectory preparation is not fully reproducible.

Citations

Before publishing, open Help → Guide & Citations… → Citations. Cite VMDHole, VMD, and HOLE. Add citations for any additional method used, such as Connolly, ellipse fitting, hydration, or a property scale. See References for the full entries.

Continue with the Pore workflow for trajectory operation and additional pore analysis views.