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from pymol import cmd
from random import random
import time
# this shows how you can efficiently update the coordinates
# of an existing model for real-time viewing
# for asychronous execution, you want to run this using the "spawn"
# command from inside PyMOL or with the "-l" option from the unix shell
# WARNING: if you do not run this using "spawn" or the "-l" option,
# PyMOL will freeze, will not refresh the workspace, and might be difficult
# to recover.
# To run this script so that you can stop it, run with the global option:
#
# spawn chempy_model02.py, global
#
# Then you have access to the "cont" variable, and can stop the loop by
# simply setting it:
#
# cont = False
#
cont = False
# first we need a model
if os.path.exists("$PYMOL_PATH/test/dat/pept.pdb"):
cmd.load("$PYMOL_PATH/test/dat/pept.pdb","demo")
else:
from inspect import getsourcefile
current_file_dir = os.path.dirname(os.path.abspath(getsourcefile(lambda:0)))
cmd.load(os.path.join(current_file_dir, "../../test/dat/pept.pdb"), "demo")
# let's dress it up a little bit
cmd.show("sticks","demo")
cmd.show("spheres","resi 10")
cmd.color("yellow","resi 5 and element C")
# turn off some of the chatter about reloading the object...
cmd.feedback("disable","executive","actions")
# now loop, updating the coordinates and reloading the model into
# state 1 of the "demo" object
m = cmd.get_model()
while cont:
time.sleep(0.05)
try:
cmd.set("suspend_updates","1") # only necessary if multithreading...
for a in m.atom:
a.coord[0]+=(random()-0.5)*0.1
a.coord[1]+=(random()-0.5)*0.1
a.coord[2]+=(random()-0.5)*0.1
cmd.load_model(m,"demo",1)
cmd.set("suspend_updates","0") # only necessary if multithreading...
except:
cmd.set("suspend_updates","0") # only necessary if multithreading...
traceback.print_exc()
cmd.refresh()
# Summary: this is portable, safe, but inefficient. For real-time visualization
# of coordinate changes, there is a way to do this by passing in an opaque
# C data structure...
# Cheers, warren@delanoscientific.com
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