Hello,

I have three intramolecular tunnels in three pymol session (.pse) files. Two .pse files are corresponding to the same snapshot in molecular dynamics. The third .pse file is 
for a different snapshot. I want to merge these .pse files using commands like

load first.pse
load second.pse,partial=1
load third.pse,partial=1

The problem is the third.pse file which is corresponding to a different snapshot in molecular dynamics is not aligning properly if I do like above. Could anyone please advise
me on how to align all the three .pse files  into one merged .pse file? I highly appreciate your help.

Thank you

Sajeewa Dewage