Mingfeng Yang wrote:
>
> UCSF Chimera is a really great replacement of VMD. Compatible with
> Amber data format, very user friendly.
> And certainly you can make a movie with it.
>
> Mingfeng
I wasn't going to comment on this because the movie-making functionality
isn't fully fleshed out in UCSF Chimera yet, but
the movie-viewing functionality definitely is. The "MD Movie extension"
which is part of UCSF Chimera llows you to
view AMBER format (new and old prmtop), CHARMM, GROMOS, MMTK, PDB, NAMD,
and XPLOR formatted
movies.
I've written a script that automates the process of rendering movie
frames; I use this script in conjuction with a cluster of compute
nodes that have fast OpenGL cards to remotely render very long movies.
The script basically loads individual trajectory frames,
renders them attractively, and saves the rendered images to files which
can then be assembled using standard movie-making programs.
Here is the script; you'll have to know python, and a bit about Chimera,
to make it do what you want. Run the script something like this:
HOSTNAME=pabst.lbl.gov DISPLAY=:1 START=0 STOP=5 WIDTH=640 HEIGHT=480
PRMTOP=~/src/topoI/INPUT/topoI.top TRAJECTORY=x.traj
MOVIE_BASE=movie_scratch ~/sw/chimera/chimera-1.2172/bin/chimera
scripts/movie.py
## chimera script to make PNG files from an Amber trajectory
import Tkinter, chimera, Midas, Trajectory, gzip
from Trajectory.formats.Amber.Amber import Amber
import os, sys, time, traceback, string
#from PIL import Image
from chimera.printer import saveImage
from chimera import dialogs
class MovieCallbacks:
def __init__(self, f, reply_dialog):
self.f = f
self.reply_dialog = reply_dialog
def init_callback(self, start, stop):
self.start = start
self.stop = stop
# dialogs.display(tkgui._ReplyDialog.name)
def size_callback(self):
if self.reply_dialog:
x = "-1-1"
# d = dialogs.find(tkgui._ReplyDialog.name)
# d.uiMaster().winfo_toplevel().wm_geometry(x)
def render_callback(self, frame):
pass
class MDMovieCallbacks(MovieCallbacks):
def __init__(self, f, reply_dialog, prmtop, trajectory):
MovieCallbacks.__init__(self, f, reply_dialog)
self.prmtop = prmtop
self.trajectory = trajectory
self.bondColor = chimera.MaterialColor()
self.bondColor.ambientDiffuse = (0.0, 0.8, 0.9)
self.bondColor.opacity = 1
def init_callback(self, start, stop):
MovieCallbacks.init_callback(self, start, stop)
self.ensemble = Amber(self.prmtop, self.trajectory, None, None)
self.frames_done = 0
if self.start > len(self.ensemble) or self.stop >
len(self.ensemble):
raise RuntimeError, "Cannot set start (%d) or stop (%d)
greater than length of ensemble (%d)" % (self.start, self.stop,
len(self.ensemble))
if self.start < 0 or self.stop < 0 or self.start >= stop:
raise RuntimeError, "Cannot set start (%d) or stop (%d) to
less than 0 or start greater than or equil to stop" % (self.start,
self.stop)
self.frames_total = self.stop - self.start
self.molecule = Trajectory.Ensemble(self.ensemble)
self.molecule.CreateMolecule()
self.molecule.LoadFrame(1)
self.molecule.AddMolecule()
self.refmolecule = Trajectory.Ensemble(self.ensemble)
self.refmolecule.CreateMolecule()
self.refmolecule.LoadFrame(1)
self.refmolecule.AddMolecule()
Midas.turn("x", -25)
Midas.turn("z", 25)
Midas.turn("y", 40)
Midas.undisplay("#1")
Midas.ribbon("#0")
Midas.undisplay("#0")
Midas.ribcolor("red", "#0:/isHelix")
Midas.ribcolor("blue", "#0:/isSheet")
Midas.window("#1")
Midas.scale(2)
Midas.wait(1)
self.t0 = time.time()
def size_callback(self):
MovieCallbacks.size_callback(self)
x = "%dx%d+0+0" % (width+8, height+78)
# chimera.tkgui.app.winfo_toplevel().wm_geometry(x)
def render_callback(self, frame):
try:
self.molecule.deleteCoordSet(self.molecule.coordSets[frame])
except:
pass
self.molecule.LoadFrame(frame+1)
Midas.match("#0:1-545", "#1:1-545")
Midas.undisplay("#0")
Midas.color("byatom", "#0")
Midas.undisplay("#0.=H=")
Midas.wait(1)
t = time.time()
pct_complete = self.frames_done/float(self.frames_total)*100
if self.frames_done:
time_to_complete = (t-self.t0)/self.frames_done *
(self.frames_total-self.frames_done)
else:
time_to_complete = 0
self.f.write("Rendered frame %d (%d of %d, %d-%d), %5.2f%%
complete, %5.2f seconds remaining)\n" % (frame, self.frames_done,
self.frames_total, start, stop, pct_complete, time_to_complete))
self.f.flush()
self.frames_done += 1
return True
class Movie:
def __init__(self, f, callbacks, movie_base, start, stop):
self.f = f
self.callbacks = callbacks
self.movie_base = movie_base
self.start = start
self.stop = stop
def init(self):
self.callbacks.init_callback(self.start, self.stop)
def size(self):
self.callbacks.size_callback()
def run(self):
for i in range(self.start, self.stop):
path = os.path.join(self.movie_base, "image.%06d.jpg" % i)
if not os.path.exists(path):
self.f.write("rendering frame: %d\n" % i)
self.f.flush()
self.callbacks.render_callback(i)
self.snapphoto(path)
else:
self.f.write("not rendering frame: %d\n" % i)
def snapphoto(self, path):
Midas.wait(1)
saveImage(path, width, height, format="PNG")
self.f.flush()
f = open("chimera.%s" % os.getenv('HOSTNAME'), "w")
#f = sys.stdout
## start = int(sys.argv[1])
## stop = int(sys.argv[2])
## start = 0
## stop = 1
host = os.getenv("HOSTNAME")
display = os.getenv("DISPLAY")
start = os.getenv("START")
stop = os.getenv("STOP")
width = os.getenv("WIDTH")
height = os.getenv("HEIGHT")
prmtop = os.getenv("PRMTOP")
trajectory = os.getenv("TRAJECTORY")
movie_base = os.getenv("MOVIE_BASE")
f.write("%s\n" % str((host, display, start, stop, width, height, prmtop,
trajectory, movie_base)))
if not host or not display or not start or not stop or not height or not
width or not prmtop or not trajectory or not movie_base:
f.write("Error: environment variables not defined\n")
f.write("%s\n" % map(lambda x: (x, os.getenv(x)), ['HOSTNAME',
"DISPLAY", "START", "STOP", "WIDTH", "HEIGHT", "PRMTOP", "TRAJECTORY",
"MOVIE_BASE"]))
sys.exit(1)
start, stop, width, height = map(int, (start, stop, width, height))
f.write("Doing job on %s, display: %s, start: %d, stop: %d, movie_base:
%s\n" % (host, display, start, stop, movie_base))
f.flush()
try:
md = MDMovieCallbacks(f, 1, prmtop, trajectory)
m = Movie(f, md, movie_base, start, stop)
m.init()
m.size()
m.run()
except:
error_status = sys.exc_info()
map(f.write, traceback.format_exception(error_status[0],
error_status[1], error_status[2]))
f.flush()
sys.exit(1)
sys.exit(0)
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Received on Tue Nov 08 2005 - 19:53:01 PST
