RE: [PyMOL] How to run PyMol from within Python?
> So there is no way to run and control PyMol from within > another python program? If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program as shown in examples/devel/start_pymol.py. However, this is not recommended because the PyMOL launch sequence is not fixed. If you do use it, be prepared to deal with changes down the road. > The reason for asking is that we are working on a python platform to > run and evaluate protein-protein docking calculations. It would be a > nice feature to be able to call up interaction surfaces and > protein-protein clusters for display in PyMol and then interact with > them from within our program. > As things are now I'm forced to treat PyMol as I would treat any > molecular graphics program, that is write macros macros for it. This > is of course much less convenient and less flexible compared to > running PyMol from within our python code. > Has anyone been able to run and quit PyMol from within python without > killing the interpreter? Is it possible? How? The underlying source of the limitation here is that the GLUT and Tcl/Tk libraries which PyMOL uses do not support repeated set-up/take-down -- they are both static "global" systems which steal threads and never return. Thus, while PyMOL is not inherently limited in this fashion, these building blocks which it employs are. Eventually there will be versions of PyMOL which are both GLUT and TCL/Tk independent -- but not today. Instead, I recommend using some kind of inter-process communication along with object serialization to pass data from your program into PyMOL. Python makes this relatively easy, but you are looking at a little bit of development. Sorry the news isn't better! Warren
Re: [PyMOL] pymol without GL
Nathaniel Echols wrote: By the way, has anyone else experimented with hardware antialiasing on NVidia cards under Linux? I've had mixed results so far, and I'm not sure what I'm doing wrong (this is with a GeForce 4 Ti 4600). the nvidia driver (as far as 28.90) does not allow for simultaneous use of anti-aliasing and depth-cueing (fog) so you must choose either one of those, not both from within pymol. zac
Re: [PyMOL] pymol without GL
> pymol.com -c scriptname > But you have to get your view first somehow. I can't do this until I compile it; if I try running a pre-existing build I get errors because one of the GL libraries isn't found. I've ended up just installing GL on my system, but the crack technical wizards at SuSE have decided I need Qt and KDE as well. . . on web server. *sigh* It's not really important that I be able to do this, and there's plenty of disk space to spare, but I prefer limited installs on a server. By the way, has anyone else experimented with hardware antialiasing on NVidia cards under Linux? I've had mixed results so far, and I'm not sure what I'm doing wrong (this is with a GeForce 4 Ti 4600). -Nat
Re: [PyMOL] pymol without GL
Hello: pymol.com -c scriptname But you have to get your view first somehow. Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca * On Tue, 16 Jul 2002, Nathaniel Echols wrote: > > quick question: I'm trying to do batch jobs on a server. Obviously, > there's no X or OpenGL installed. Is there any way to build PyMOL without > any graphical frontend, and just use it as a raytracer? I don't want to > go through the trouble of adding in these libraries... > > thanks, > Nat > > > > --- > This sf.net email is sponsored by: Jabber - The world's fastest growing > real-time communications platform! Don't just IM. Build it in! > http://www.jabber.com/osdn/xim > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *
[PyMOL] pymol without GL
quick question: I'm trying to do batch jobs on a server. Obviously, there's no X or OpenGL installed. Is there any way to build PyMOL without any graphical frontend, and just use it as a raytracer? I don't want to go through the trouble of adding in these libraries... thanks, Nat
[PyMOL] Re: How to run PyMol from within Python?
Johan,
"JL" == Johan Leckner wrote:
JL> So there is no way to run and control PyMol from within another python
JL> program?
Why? There is!
[...]
JL> Has anyone been able to run and quit PyMol from within python without
JL> killing the interpreter? Is it possible? How?
Here's a script, that I've used to use in Nov. Not sure that it will run
with current version of pymol, however.
# -*- python -*- file
# $Id: mov.py,v 1.8 2001/11/23 23:47:48 akhavr Exp $
#
# Copyright (C) 2001 by KDS Software Group http://www.kds.com.ua/
from glob import glob
import os
import sys
def split(movie_name):
movie = open(movie_name)
filename = "output"
counter = 1
f = open(filename+"%010d" % counter,"w")
skipnextline = 1
while 1:
l = movie.readline()
if l == "":
break
if l == " \r\n" or l == " \n":
f.close()
counter = counter + 1
f = open(filename+"%010d" % counter,"w")
skipnextline = 1
continue
if skipnextline == 1:
skipnextline = 0
continue
else:
f.write(l)
f.close()
os.remove(filename+"%010d" % counter)
def make_pdb():
for file in glob("output*"):
os.system("transform 5 "+file+" "+file+".xyz")
os.system("babel -ixyz "+file+".xyz -opdb "+file+".pdb")
os.remove(file+".xyz")
os.remove(file)
def def_movie(width,height):
file_list = glob("output*.pdb")
for file in file_list:
cmd.load(file, "mov")
cmd.move("z",-10)
cmd.hide("lines")
cmd.show("spheres")
mov_def = ""
for i in range(1, len(file_list)+1):
mov_def = mov_def + str(i) + " "
cmd.mset(mov_def)
cmd.viewport(width,height)
cmd.bg_color("white")
def make_png():
if not os.path.exists("png"): os.mkdir("png")
# enable raytracing
cmd.set("ray_trace_frames",1)
cmd.set("cache_frame",0)
# render
cmd.mpng("png/mov")
def make_yuv():
os.chdir("png")
for i in glob("*"):
( base, suffix ) = re.split('_', i)
( no, suffix ) = re.split('\.', suffix)
yuv_name = base+"."+str(int(no))
os.system("pngtopnm "+i+" | ppmtoyuvsplit "+yuv_name)
os.chdir("..")
def make_avi(width, height):
os.chdir("png")
num = str(len(glob("mov*Y")))
os.system("mpeg -a 1 -b "+num+" -h "+str(width)+" -v "+str(height)+
" -PF mov. -s mov.mpg")
os.system("ffmpeg -f mpegvideo -i mov.mpg -r 25 " +
"-an -f avi -b 1000 mov.avi ")
try:
os.remove("../mov.mpg")
os.remove("../mov.avi")
except OSError: pass
os.rename("mov.mpg","../mov.mpg")
os.rename("mov.avi","../mov.avi")
os.chdir("..")
def clean():
for file in glob("output*"):
os.remove(file)
for file in glob("png/*"):
os.remove(file)
os.rmdir("png")
width=800
height=600
try:
movie_name = sys.argv[3]
print "Processing "+movie_name
split(movie_name)
make_pdb()
def_movie(width,height)
make_png()
make_yuv()
make_avi(width,height)
clean()
except IndexError:
print """
Usage:
pymol -c mov.py z-sequence-file
"""
--
Andrey V Khavryuchenko http://www.kds.com.ua/
Software Solutions
Re: [PyMOL] How to run PyMol from within Python?
Hi all, So there is no way to run and control PyMol from within another python program? The reason for asking is that we are working on a python platform to run and evaluate protein-protein docking calculations. It would be a nice feature to be able to call up interaction surfaces and protein-protein clusters for display in PyMol and then interact with them from within our program. As things are now I'm forced to treat PyMol as I would treat any molecular graphics program, that is write macros macros for it. This is of course much less convenient and less flexible compared to running PyMol from within our python code. Has anyone been able to run and quit PyMol from within python without killing the interpreter? Is it possible? How? Cheers, Johan > I'm having problems running PyMol from within another Python program. This is not the recommended way to run PyMOL and may lead to problems. You can run Python programs within PyMOL as follows: from the command-line: pymol example.py # synchronous, in PyMOL module pymol -r example.py # synchronous in __main__ module pymol -l example.py # asychronous in a new module You can also launch python programs from within PyMOL with the commands: run example.py# synchronous in pymol module run example.py,main # synchronous in __main__ module spawn example.py# asychronous in a new module spawn example.py,global # asychronous in the PyMOL module spawn example.py,main # asychronous in the __main__ module see: help launching help run help spawn > Following the examples in /pymol/examples/devel I have been able to > launch and controll PyMOL. The problem occur when I try to quit PyMol > (version. 0.82) however I do it I end up with a fault terminating my > Python interpreter. > > Under Redhat 7.1/Python 2.1 i get a segmentation fault and under > MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same > result both when quitting from the gui or within python with the > command cmd.quit() > > How can I quit PyMol properly? I know for a fact that the Mac take-down process is currently flawed, and frequently gives a bus error. Because it only happens after you quit the program, its a low priority issue... Not sure about Redhat. Warren
