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 directoriesconfig_file = "config.xml"trajectory_file = "brush.dcd"image_file = "final_config.png"# Write VMD commands to a script filevmd_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 filevmd_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)