I am attempting to write a script that isolates beads of a certain name and adjusts their draw style before running the trajectory animation and taking a snapshot of the final configuration. the snapshot is no issue but i cannot figure out how to change my representation in the way i can with the normal interface. I just want to set the representation selection to “name A B C and z>0” and change draw style to VDW before taking the snapshot.

The script im using is below, i dont have a lot of experience but from what i understand it just runs vmd and gives it a .tcl file to tell it what to do. When attempting to isolate my selection i can only manage to select the atoms to retrieve info, not actually change the representation itself.

import subprocess

# Set the file names and directories
config_file = "config.xml"
trajectory_file = "brush.dcd"
image_file = "final_config.png"

# Write VMD commands to a script file
vmd_script_file = "vmd_script.tcl"


commands = [
    f"mol addfile {trajectory_file}",  # Load the trajectory file into the current molecule

*representation commands here*

    "animate goto end",
    f"render snapshot {image_file}"  # Take a snapshot and save it to the current directory
]

with open(vmd_script_file, "w") as script:
    script.write("n".join(commands))

# Set the VMD command to open the file
vmd_command = f"vmd -hoomd {config_file} -e {vmd_script_file}"

try:
    # Run VMD with the combined set of commands
    process = subprocess.Popen(vmd_command, shell=True)
    process.wait()

except subprocess.CalledProcessError as e:
    print("Error:", e)