Script VMD
with GUI,
vmd *.pdb text -e vmd_visualize.tcl
without GUI
vmd -dispdev text *.pdb -eofexit < ../../script.tcl
Hutch Polecat
with GUI,
vmd *.pdb text -e vmd_visualize.tcl
without GUI
vmd -dispdev text *.pdb -eofexit < ../../script.tcl