VMD-L Mailing List

From: Peng Tao (vmdhelp_at_gmail.com)
Date: Thu Aug 03 2006 - 11:23:03 CDT

Dear John and Axel,

I just upgraded my VMD to the newest production version. It seems working
for me!
I successfully launched IED window!

Thank you all for your kind help and suggestions!

Best regards,
Peng Tao

On 8/3/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Hi,
> You'll need to use the final release version of VMD 1.8.4, the
> beta 9 version you're running is out of date and used an older Python
> build which may explain some of your problems. I didn't notice this
> with your previous email, but for the test you listed below, that's
> going to cause problems. When a production version of VMD is released
> I always recommend people to stop using the old test versions....
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Aug 03, 2006 at 10:47:21AM -0400, Peng Tao wrote:
> > Dear John,
> >
> > Now I am also trying to run IED in VMD on my local Linux box. There
> should
> > not be DISPLAY problem in this way. I installed precompiled library
> > pylib.linux.tar.gz<
> http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/vmd-1.8.4/pylib.linux.tar.gz
> >,
> > and set PYTHONPATH to that directory: (setenv PYTHONPATH
> > /scr/ptao/tools/vmd/prelib/lib_LINUX-rh9), and reinstalled precomplied
> VMD.
> > Unfortunately, there is still no luck here.
> > Any luck that I can get IED work for me without recompling VMD from
> source
> > code?
> >
> > Info) VMD for LINUX, version 1.8.4b11 (February 10, 2006)
> > Info) http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 1 CPU detected.
> > Info) OpenGL renderer: Mesa GLX Indirect
> > Info) Features: RN MTX
> > Info) GLSL rendering mode is NOT available.
> > Info) Textures: 2-D (2048x2048), Multitexture (6)
> > vmd > gopython /scr/ptao/tools/ied/ied-2.02/ied.py
> > Info) Starting Python...
> > Info) Text interpreter now Python
> > Traceback (most recent call last):
> > File "VMD", line 21, in ?
> > File "/scr/ptao/lib/vmd/scripts/python/Tkinter.py", line 59, in ?
> > import _tkinter # If this fails your Python may not be configured for
> > Tk
> > ImportError: No module named _tkinter
> > Info) Text interpreter now Tcl
> > Traceback (most recent call last):
> > File "<string>", line 2, in ?
> > AttributeError: 'module' object has no attribute 'tkinter'
> > vmd >
> >
> >
> >
> >
> > On 8/2/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > >
> > >Hi,
> > >You mentioned you're running VMD from a remote system. Have
> > >you verified that you've got the DISPLAY environment variable
> > >properly set before running VMD? It's possible that Python and
> > >TkInter aren't getting it for some reason even though VMD itself
> > >and the Tcl-based plugins are. I assume that the other windows
> > >display with no problem?
> > >
> > >Thanks,
> > >John Stone
> > >vmd_at_ks.uiuc.edu
> > >
> > >
> > >On Wed, Aug 02, 2006 at 10:13:04PM -0400, Peng Tao wrote:
> > >> Dear VMD user,
> > >>
> > >> It sounds stupid, but I still could not get IED work for me after
> > >reading
> > >> all of the posts about IED in the mailing list.
> > >>
> > >> I am trying to run IED on a remote super computer center (with Linux
> > >> 2.6.17.6 kernal). My local machine is Redhat9. I installed
> precompiled
> > >> library
> > >> pylib.linux.tar.gz<
> > >
> http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/vmd-1.8.4/pylib.linux.tar.gz
> > >>
> > >> from
> > >>
> > >> http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/
> > >> And reinstalled precompiled VMD.
> > >>
> > >> But I still could not run IED. At the end, VMD is not complaining
> either
> > >> numpy or tkinter.
> > >> ut I don't know what's wrong with 'Frame'. I really need to use IED.
> But
> > >I
> > >> don't have administrator privilige any where. Recompiling VMD from
> > >source
> > >> code is not an option for me.
> > >> Is there any thing I can do to get IED work for me?
> > >>
> > >> Thank you very much.
> > >>
> > >> Best regards,
> > >> Peng Tao
> > >>
> > >> Info) VMD for LINUX, version 1.8.4a22 (October 11, 2005)
> > >> Info) http://www.ks.uiuc.edu/Research/vmd/
> > >> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > >> Info) Please include this reference in published work using VMD:
> > >> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > >> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > >> Info) -------------------------------------------------------------
> > >> Info) Multithreading available, 4 CPUs detected.
> > >> Info) OpenGL renderer: Mesa GLX Indirect
> > >> Info) Features: RN MTX
> > >> Info) GLSL rendering mode is NOT available.
> > >> Info) Textures: 2-D (2048x2048), Multitexture (6)
> > >> vmd > gopython /a/osu3112/tools/IED/ied-2.02/ied.py
> > >> Info) Starting Python...
> > >> Info) Text interpreter now Python
> > >> Traceback (most recent call last):
> > >> File "VMD", line 21, in ?
> > >> File "/a/osu3112/bin_p4/lib/vmd/scripts/python/Tkinter.py", line 59,
> in
> > >> ?
> > >> import _tkinter # If this fails your Python may not be configured
> for
> > >> Tk
> > >> ImportError: No module named _tkinter
> > >> Info) Text interpreter now Tcl
> > >> Traceback (most recent call last):
> > >> File "<string>", line 2, in ?
> > >> AttributeError: 'module' object has no attribute 'tkinter'
> > >> vmd > gopython /a/osu3112/tools/IED/ied-2.02/ied.py
> > >> Info) Text interpreter now Python
> > >> Traceback (most recent call last):
> > >> File "VMD", line 466, in ?
> > >> AttributeError: 'module' object has no attribute 'Frame'
> > >> Info) Text interpreter now Tcl
> > >> vmd > gopython /a/osu3112/tools/IED/ied-2.02/ied.py
> > >> Info) Text interpreter now Python
> > >> Traceback (most recent call last):
> > >> File "VMD", line 466, in ?
> > >> AttributeError: 'module' object has no attribute 'Frame'
> > >>
> > >> Info) Text interpreter now Tcl
> > >
> > >--
> > >NIH Resource for Macromolecular Modeling and Bioinformatics
> > >Beckman Institute for Advanced Science and Technology
> > >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > >WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
> >
> >
> >
> > --
> > Best regards,
> > Peng Tao
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
Best regards,
Peng Tao