Questions about the outputs of gmx_clusterByFeatures hole program

[stephaneabel]

Dear Dr Kumar

I wish you a Happy New Year. Now my questions

For my work I would like to compute the "average" pore radius for a given system for given time period (say 100 - 200 ns) and I have two questions about the outputs of gmx_clusterByFeatures hole program.

1. Are the printed values (lines with the " (sampled) " and "(mid-point) " fields) on display terminal give the "average" pore radius along the z axis for this time period?

2. I understand that -pdb argument of the gmx_clusterByFeatures hole provides the structure of the pore for each time frame (here between 100 ns -- 200 ns) in the PDB format. It is possible to obtain from pdb the "average" structure of the pore (also in the PDB format) for the mentioned time period that can be used, for instance for plotting with Pymol? If yes how

Thank you for your response

Best

Stéphane