VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 03 2006 - 11:30:01 CDT

Excellent, I'm glad that solved it for you.

This should serve as a cautionary tale to those of you that are still
running ancient test versions :-)

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 03, 2006 at 12:23:03PM -0400, Peng Tao wrote:
> 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beta 9 version you're running is out of date and used an older Python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 

-- 
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