From: Aryan Vahedi (
Date: Fri Apr 03 2015 - 11:24:56 CDT


I am investigating the interaction of a protein with CNT. I have run a simulation for 100 ns and can see that the protein is adsorbing onto the surface on the CNT. Using the Graphical Representations GUI I can visually identify possible contact residues using the selection:

protein and within 1.5 of resname CNT

Then after choosing "Update Selection After Every Frameā€ under Trajectory (in Graphical Representations) and setting an appropriate Drawing Method I can clearly see which atoms come into that distance over the course of the trajectory.

My question is what is the series of command I can use in the Tk console to quickly identify these residues. I use:

$sel1 get resid resname

But this only gives me the selection (protein and within 1.5 of rename CNT) I made at a particular frame. What command can I use to identify (i.e. have them printed in the console) the residues that fall within 1.5 A of the CNT over the course of the entire trajectory I have loaded in?

Many Thanks for Your Help,
Aryan Vahedi
MS Biology
Morgan State University