VMD-L Mailing List

From: Ropón-Palacios G. (groponp_at_gmail.com)
Date: Thu Sep 21 2023 - 16:21:11 CDT

Dear All,

I am trying to measure the exact size that I need to solvate a protein inserted in a membrane, then I came across the simple charmm-gui solution that measures the cross section and adds a padding (according to the user's need), that is, if I measure in the xy e minmax plane of the protein, choose the largest value and add pad (i.e. if it were pad/2 on each side), now when I was looking at the vmd commands, I have the option of using [measure minmax $sel] and [measure minmax $sel -withradii], what is the difference and which of them would be more appropriate when calculating this value for solvating in general.

best,

Geo.