[MMTK] Re: MMTK Windows Problems

Konstantinos Makrodimitris kmakr7 at msn.com
Fri Jul 11 22:03:02 EDT 2003


Hi,

>Date: Fri, 20 Jun 2003 11:41:54 -0500
>From: "John Michelsen" <jmichelz at mail.com>
>Subject: [MMTK] Re: MMTK Windows Problems
>To: mmtk at python.net
>Message-ID: <20030620164154.40367.qmail at mail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
> > There is a also a little confusion why the visualization examples don't
> > work.  >
> > C:\MMTK22\Examples\Visualization>python additional_objects.py
> > Traceback (most recent call last):
> >   File "additional_objects.py", line 38, in ?
> >     scene.view()
> >   File "C:\Python22\Lib\site-packages\Scientific\Visualization\VRML.py",
> > line 149, in view
> >     import win32api
> > ImportError: No module named win32api
> >
> > I have valued of course the environment variable PDBVIEWER
> > the file name of the executable, and must give "vmd"  after stripping 
>off an
> > optional directory specification and iinstalled VMD.
>
>The win32api thing was probably from me, try installing win32all from Mark 
>Hammond.
>This is a wrapper library that lets you access a lot of windows specific 
>stuff from python.
>http://starship.python.net/crew/mhammond/win32/Downloads.html
>(Konrad, maybe you could put a note to that effect on the website for other 
>windows users.)


I had valued the PDBVIEWER in order to have eg

>>>os.environ['PDBVIEWER']
'C:\\Program Files\\University of Illinois\\VMD\\vmd'

I am trying this example Ffor Visulaization in MMTK-examples modified for 
VMD instead of VRML:
_________________________________________________
from Scientific.Visualization import VMD; module = VMD
protein = Protein('insulin')
center, inertia = protein.centerAndMomentOfInertia()
mass = protein.mass()
diagonal, directions = LinearAlgebra.eigenvectors(inertia.array)
diagonal = Numeric.sqrt(diagonal/mass)
graphics = protein.graphicsObjects(graphics_module = module,
                                   model = 'backbone', color = 'red')
valines = protein.residuesOfType('val')
sidechains = valines.map(lambda r: r.sidechain)
graphics = graphics + sidechains.graphicsObjects(graphics_module = module,
                                                 model='wireframe',
                                                 color = 'blue')
for length, axis in map(None, diagonal, directions):
    graphics.append(module.Arrow(center, center+length*Vector(axis), 0.02,
                                 material=module.EmissiveMaterial('green')))
scene = VMD.Scene(graphics)
scene.view()
>>>

The system cannot find the path specified.
>>>
______________________________________________

Why? Is the path just the executable of VMD with the directory specified 
please?


I'd like to ask also if there is any answer to why the MolecularDynamics
give MEMORYERROR in Windows installations:

________________________________________________________________
#### C:\MMTK22\Examples\MolecularDynamics>PYTHON  solvation.py
30 water molecules will be added
Solvent molecules have been added, now shrinking universe...
Traceback (most recent call last):
  File "solvation.py", line 60, in ?
    MMTK.Solvation.shrinkUniverse(universe, temperature, 'solvation.nc')
  File "C:\Python22\Lib\site-packages\MMTK\Solvation.py", line 112, in 
shrinkUniverse
    snapshot()
  File "C:\Python22\Lib\site-packages\MMTK\Trajectory.py", line 1261, in 
__call__
    snapshot(self.universe, data, actions, energy_terms)
MemoryError

#### C:\MMTK22\Examples\MolecularDynamics>PYTHON protein.py
Temperature:  54.2066847637
Momentum:  [-0.96671630605968883, 7.3114006253079165, -5.319160412233904]
Angular momentum:  [-1.6358556712649883, 1.692950514307761, 
1.5823852748279084]
Step 0
Time: 0.000000
Potential energy: -80.205828, Kinetic energy: 14.873097
….
Traceback (most recent call last):
  File "protein.py", line 51, in ?
    0, None, 2),
  File "C:\Python22\Lib\site-packages\MMTK\Dynamics.py", line 189, in 
__call__
    apply(MMTK_dynamics.integrateVV, args)
MemoryError
________________________________________________________________



> > I am wondering if it is possible the MMTK developers could concern for 
>the
> > increasing interest of MMTK in Windows and could give more detailed and
> > carefull instructions of installing in Windows this utility.
> > There is a lot of mess with issues where to put Scientific, NetCDF,
> > which compiler, which update and version etc..
> > Eg when I need to install Numerics in Python I just have
> > to install the respective .exe and there is not such complications and
> > prerequisites.
>
>This is something I might look at when I get some free time in a month or 
>so.
>Should I set up a paypal link somewhere to let people know I could be 
>persuaded by tips? =)

It looks a good idea and I could help you  perhaps in Windows, C++ stuff.

Best,
Konstantinos

___________________________________________________
Dr Konstantinos DE Makrodimitris
     Research Associate, University of Virginia, Chemical Engineering
     Visiting Scientist, Johns Hopkins Medical University, Physiology

_________________________________________________________________
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