VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Thu Aug 07 2003 - 09:40:55 CDT

Paul,

There is no animate.py, atomselection.py, etc., just as there is
no sys.py in the Python libraries even though you can "import sys".
That's because these are statically-linked modules compiled into the
binary, rather than source files that are byte-compiled when imported.

Wait a minute: did you type "python" or "gopython" inside of VMD
to get to the Python interpreter? If you typed python, that would
explain everything we're seeing. Be sure to use "gopython" to enter
VMD's built-in Python interpreter; otherwise you're just executing the
external Python shell, which has no knowledge of VMD's Python extensions.

If that's not the case, please copy and paste into an email to us
everything VMD prints at startup in the text console as you enter the
Python interpreter inside VMD and try to import the VMD module.

Thanks,
Justin

On Thu, Aug 07, 2003 at 09:28:12AM +0100, barrett wrote:
> John, Justin
>
> Thankyou both for your involvement.
>
> I have included versions and platforms below, which I hope will help you
> help me.
>
> Just a note before you look at them: whilst I may possibly have
> PYTHONHOME wrong the problem is more profound than that: I cannot even
> find animate.py, atomselection.py etc on my hard drive. They just don't
> seem to be there.
>
> ???Where would you expect them to be???
>
> Version Information:
>
> VMD:
> I am currently running 1.8.1.
> I have previously run 1.8 and 1.6
> In none of the installations of the software (1.8, 1.8.1, 1.6) have I
> been able to locate those files.
>
> Python:
> Python 2.2.1 (#1, Aug 30 2002, 12:15:30)
> [GCC 3.2 20020822 (Red Hat Linux Rawhide 3.2-4)] on linux2
>
> Platform:
> VMD Atholon MP2200+
>
> Thanks again: I would be very happy if we manage to fix this.
>
> Paul
>
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: 06 August 2003 17:02
> To: barrett
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: python: cannot find library
>
>
> Dear Paul,
> Can you tell us what version of VMD you're running, and on which
> platform?
> We should be able to provide more help once we know what version and OS
> you're running with. The more info the better.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Aug 06, 2003 at 10:53:06AM +0100, barrett wrote:
> > Hi
> >
> > I would like to run Python in VMD.
> > To first order it works: e.g.
> >
> > >>>import string
> >
> > is successful and other scripts run fine.
> >
> > *However* when I try to import VMD I get:
> >
> > >>> import VMD
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in ?
> > File "/lmb/flint/barrett/local/lib/scripts/python/VMD.py", line 10,
> in
> > ?
> > import animate
> > ImportError: No module named animate
> >
> > Having searched my directories I do not seem to have animate.py, nor
> any
> > of the other modules listed below. Please can anyone tell me how to
> get
> > /find them?
> >
> > Missing modules:
> > animate
> > atomselection
> > color
> > display
> > graphics
> > imd
> > label
> > material
> > molecule
> > molrep
> > render
> > trans
> > vmdcallbacks
> >
> >
> > Many thanks
> >
> > Paul
> >
> > Dr Paul Barrett
> > Laboratory of Molecular Biophysics
> > Department of Biochemistry
> > University of Oxford
> > Oxford
> > OX1 3QU
> >
> > Tel 01865 275191
> > Fax 01865 275182
> >
> > <mailto:barrett_at_biop.ox.ac.uk> barrett_at_biop.ox.ac.uk
> > <mailto:hellopaul1_at_hotmail.com> hellopaul1_at_hotmail.com
> >
> >
>
> --
> 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
> ------------------------------------------------------------------------
> --------
> Return-Path: <johns_at_moline.ks.uiuc.edu>
> Received: by biop.ox.ac.uk (MX V4.2 AXP) with SITE; Wed, 06 Aug 2003
> 17:06:35
> +0100
> Received: from tx0.oucs.ox.ac.uk by nutmeg.biop.ox.ac.uk (MX V4.2 AXP)
> with
> SMTP; Wed, 06 Aug 2003 17:06:35 +0100
> Received: from scan0.oucs.ox.ac.uk ([129.67.1.162] helo=localhost) by
> tx0.oucs.ox.ac.uk with esmtp (Exim 4.20) id 19kQo6-00016H-Fq
> for
> barrett_at_biop.ox.ac.uk; Wed, 06 Aug 2003 17:06:34 +0100
> Received: from rx0.oucs.ox.ac.uk ([129.67.1.161]) by localhost
> (scan0.oucs.ox.ac.uk [129.67.1.162]) (amavisd-new, port 25)
> with
> ESMTP id 03952-06 for <barrett_at_biop.ox.ac.uk>; Wed, 6 Aug
> 2003
> 17:06:34 +0100 (BST)
> Received: from havana.ks.uiuc.edu ([130.126.120.73] helo=ks.uiuc.edu) by
> rx0.oucs.ox.ac.uk with esmtp (Exim 4.20) id 19kQo6-00016D-1l
> for
> barrett_at_biop.ox.ac.uk; Wed, 06 Aug 2003 17:06:34 +0100
> Received: from moline.ks.uiuc.edu (moline.ks.uiuc.edu [130.126.120.60])
> by
> ks.uiuc.edu (8.12.9/8.11.2) with ESMTP id h76G2OCr015987; Wed,
> 6 Aug
> 2003 11:02:24 -0500 (CDT)
> Received: (from johns_at_localhost) by moline.ks.uiuc.edu
> (8.11.6+Sun/8.9.1) id
> h76G2OY10533; Wed, 6 Aug 2003 11:02:24 -0500 (CDT)
> Message-ID: <20030806110220.F10261_at_moline.ks.uiuc.edu> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys