I need to run an script based on PyMOL  for a thousands of proteins. The problem is that even when I delete all object the RAM usage keeps increasing. I am using PyMOL 1.7 on ubuntu 14.04 (beta 2).

my script looks like this.

import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd, stored
import glob

pdb_files = glob.glob('*.pdb')
for protein in pdb_files:
        "some code here"

I tried the following.

1) removing the  "some code here"
2) adding cmd.reinitialize()
3) adding cmd.set('suspend_undo', 1) (https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11126.html)

Cheers and thanks in advance.