TCL scripts for taking snapshots from molecular simulation trajectories

Load the dcd trajectory

vmd sd*.mol2 sd*.dcd

In TKconsole:

play take_snap.tcl

Go to last frame

CapsidPolymer

Then go to the selected frame

Zoom in and make the view as desired

Then

display resize 1000 10000 Capsidpolymer

Choose a frame number as part of the filename

onesnap framenumber

To convert tga files to jpg:

Close vmd

In the folder that you have tga files run

bash convert.sh