Hi, In my python script I'm using the combine() function to merge a protein and a molecule into one model and since I'm doing this multiple times and only use the combined result to save it with pdbWrite I want to free the memory of the object combination right after that, but after the instructions chimera.openModels.close(combination), del combination, chimera.update.checkForChanges(), gc.collect(), chimera.closeSession() the memory is not freed. This is the code that reproduces the problem, it uses the molecules in the zipfile I have attatched.

import chimera

from Combine import combine

import zipfile

import time

import gc

import os

#from memory_profiler import profile

for itemnum in range(3):

#@profile

def pathmaker(itemnum):

dirpath = os.path.dirname(os.path.realpath(__file__))

zippath=dirpath+'/'+'test1_000.zip'

torsionpath=zipfile.ZipFile(zippath).extract('Pathway_000_Pathway.txt')

proteinpath=zipfile.ZipFile(zippath).extract('Protein_000_Protein.mol2')

ligandpath=zipfile.ZipFile(zippath).extract('Ligand_000_Ligand.mol2')

opened = chimera.openModels.open(proteinpath)

protein = opened[0]

opened1 = chimera.openModels.open(ligandpath)

mol=opened1[0]

combination=combine([mol,protein],protein)

totalnum=str(itemnum).zfill(3)+'_'+str(i).zfill(3)

chimera.pdbWrite([combination], chimera.Xform(), 'testpdb%s.pdb' %totalnum)

print('writing testpdb%s.pdb' %totalnum)

chimera.openModels.close(combination)

del combination

chimera.update.checkForChanges()

gc.collect()

chimera.closeSession()

for i in range(20):

pathmaker(itemnum)

#this stops the code and shows memory increase for each iteration

print('pause 6 seconds...')

time.sleep(6)