VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 03 2006 - 10:40:15 CDT

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beta 9 version you're running is out of date and used an older Python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