Abigail,

there seem to be 2 issues here. One is the errors coming from the python
scripts, the other related to guile.

1.) the python error (i.e. active_residue) is my bad, since the coot.py
file from my scripts has additional functions included which wont work
on 'normal' python built coot yet. This should go away if you delete the
lines including and after active_residue in your coot.py file. Or
replace coot.py it with attached file.

2.) with respect to guile, please try Paul's suggestions.

Bernhard   

***************************************************

Dr. Bernhard Lohkamp
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden

phone: (+46) 08-52487698
fax:   (+46) 08-327626
email: [log in to unmask]

----- Original Message -----
From: Paul Emsley <[log in to unmask]>
Date: Saturday, September 8, 2007 11:00 am
Subject: Re: [COOT] Error and failure to start upon update to 0.4
pre-release
To: [log in to unmask]

> Further thoughts:  I wonder(ed) why python would give an error like 
> that:>      ERROR: Undefined variable: class-of
> Python would interpret "class-of" as "class - of" and give a syntax 
> errorand not an undefined variable.  It is scheme that would think 
> that "class-of" 
> is a variable.  I think that the error message is popping up in the 
> wrong place
> to confuse us.
> 
> It may be that your coot is picking up (or has picked up) the wrong 
> guile.
> So, Abigail, I think there is something wrong with the .scm files 
> somewhere.If you have something in your ~/.coot file, move it aside 
> and retry.  I notice 
> that in you screen log, you don't mention the loading of .scm 
> files.  I wonder
> why that is.  Is it because you chopped it or because it didn't 
> happen?  You 
> could rename or tinker with (i.e. comment out the loading of some 
> files in)
> /sw/share/coot/scheme/coot.scm.
> 
> Paul.
> 
> 
> In message <[log in to unmask]>
> [log in to unmask] writes:
> > Sorry I didn't see this earlier.  This package works absolutely 
> fine on my
> G4s, so I don't think any of the python scripts distributed with 
> coot are
> borked.  I force it to build with the system's distributed 
> python2.3 in
> /usr/bin.  Is it possible yours is somehow non-canonical?
> > 
> > 
> > On Fri, 7 Sep 2007 14:37:02 -0700
> > Abigail LAMBERT <[log in to unmask]> wrote:
> > 
> >      When I remove "shelx.py" from the list in the 
> "coot_load_modules.py"file, the error simply moves to the 
> >      .py file previous to it in line:
> >      
> >      Loading: povray.py
> >      Loading: coot-lsq.py
> >      Loading: get-ebi.py
> >      ERROR: Undefined variable: class-of
> >      
> >      vs.
> >      
> >      Loading: povray.py
> >      Loading: coot-lsq.py
> >      Loading: get-ebi.py
> >      Loading: shelx.py
> >      ERROR: Undefined variable: class-of
> >      
> >      When I replaced all of my .py files with Bernhard's python 
> script files
> (not ALL of them, the same ones 
> >      that I had had), then the error moves to the 
> "coot_load_modules.py" file:
> >      
> >      ...
> >      There are 2 data in /sw/share/coot/lib/data/monomers/a/AD.cif
> >      There are 2 data in /sw/share/coot/lib/data/monomers/c/CR.cif
> >      There are 2 data in /sw/share/coot/lib/data/monomers/c/CD.cif
> >      There are 2 data in /sw/share/coot/lib/data/monomers/g/GR.cif
> >      There are 2 data in /sw/share/coot/lib/data/monomers/g/GD.cif
> >      There are 2 data in /sw/share/coot/lib/data/monomers/t/TD.cif
> >      There are 2 data in /sw/share/coot/lib/data/monomers/u/UR.cif
> >      Reading coordinate file: /sw/share/coot/standard-residues.pdb
> >        PDB file /sw/share/coot/standard-residues.pdb has been read.
> >      Spacegroup: P 1
> >      Cell: 40.631 109.18 93.243 90 90 90
> >      
> >      ** (coot:628): WARNING **: Couldn't find pixmap file: reside-
> info.svg>      
> >      ** (coot:628): WARNING **: Couldn't find pixmap file: env-
> distances.png>      initalize graphics molecules...initializing 
> molecules...done>      done.
> >      INFO:: loading coot.py from /sw/share/coot/python/coot.py
> >      Running python script /sw/share/coot/python/coot.py
> >      Traceback (most recent call last):
> >         File "<string>", line 1, in ?
> >         File "/sw/share/coot/python/coot.py", line 1122, in ?
> >           active_residue = _coot.active_residue
> >      AttributeError: 'module' object has no attribute 
> 'active_residue'>      INFO:: coot.py loaded
> >      INFO loading coot python modules
> >      Running python script 
> /sw/share/coot/python/coot_load_modules.py>      ERROR: Undefined 
> variable: class-of
> >      
> >      Some deprecated features have been used.  Set the environment
> >      variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
> >      program to get more information.  Set it to "no" to suppress
> >      this message.
> >      [dhcp025014:~] Abbie%
> >      
> >      It looks like I do have PyGTK installed and current.
> >      
> >      
> >      Any new ideas?
> >      
> >      
> >      
> >      
> >      
> >      
> >      On Fri, 7 Sep 2007, Paul Emsley wrote:
> >      
> >      >
> >      > Dear Abigail,
> >      >
> >      > Do let us know what Coot says when you modify it in the 
> suggestedmanner(s).
> >      >
> >      > Paul.
> >      >
> >      >
> >      >
> >      > In message 
> <[log in to unmask]>Abigail
> >      > LAMBERT <[log in to unmask]> writes:
> >      >> I'm not sure I understand what is the underlying problem 
> here (fairly
> new at
> >      > this type of computing).
> >      >> These suggestions (thanks for them) have not solved the 
> problem.  I
> have never
> >      > had such issues with
> >      >> Coot before, so why might this be coming up now, after a 
> simple upgrade?
> >      >>
> >      >> If I can understand this more thoroughly, perhaps I can 
> try and
> troubleshoot
> >      > more effectively.
> >      >>
> >      >> Thanks!
> >      >>
> >      >> Abbie
> >      >>
> >      >> On Fri, 7 Sep 2007, Bernhard Lohkamp wrote:
> >      >>
> >      >>> Didnt see that this was a python thing.
> >      >>>
> >      >>> To potentially fix this you can download my python 
> script files (
> >      >>> 
> http://www.chem.gla.ac.uk/~bernhard/coot/coot_python_scripts.tar.gz )
> >      >>> which are more up to date and shouldnt be broken. 
> Although I guess not
> >      >>> everything will work unless you have PyGTK installed. 
> And there is
> >      >>> probably a few other Python things not fixed in the 
> 'normal' coot yet.
> >      >>>
> >      >>> Bernhard
> >      >>>
> >      >>> ***************************************************
> >      >>>
> >      >>> Dr. Bernhard Lohkamp
> >      >>> Div. Molecular Structural Biology
> >      >>> Dept. of Medical Biochemistry and Biophysics (MBB)
> >      >>> Karolinska Institutet
> >      >>> S-17177 Stockholm
> >      >>> Sweden
> >      >>>
> >      >>> phone: (+46) 08-52487698
> >      >>> fax:   (+46) 08-327626
> >      >>> email: [log in to unmask]
> >      >>>
> >      >>> ----- Original Message -----
> >      >>> From: Paul Emsley <[log in to unmask]>
> >      >>> Date: Friday, September 7, 2007 10:49 am
> >      >>> Subject: Re: [COOT] Error and failure to start upon 
> update to 0.4
> >      >>> pre-release
> >      >>> To: [log in to unmask]
> >      >>>
> >      >>>> Abigail LAMBERT wrote:
> >      >>>>> Hello -
> >      >>>>>
> >      >>>>> I'm working on a PowerBook G4 Mac (PowerPC, 10.4), and 
> I updated
> >      >>>> my
> >      >>>>> Coot package in Fink.  It shows everything to be 
> successfully>      >>>> updated,
> >      >>>>> but upon startup, I get the following error: (although 
> I DO get a
> >      >>>>> glimpse of the new, nifty splash screen):
> >      >>>>>
> >      >>>>> ...
> >      >>>>> Loading: coot-lsq.py
> >      >>>>> Loading: get-ebi.py
> >      >>>>> Loading: shelx.py
> >      >>>>> ERROR: Undefined variable: class-of
> >      >>>>>
> >      >>>>>
> >      >>>> Hmm.. pythonized coot.
> >      >>>>
> >      >>>> I don't see what is going wrong.
> >      >>>>
> >      >>>> You could try to remove "shelx.py" from
> >      >>>> /sw/share/coot/python/coot_load_modules.py
> >      >>>>
> >      >>>> I'll try pythonized coot here soon.
> >      >>>>
> >      >>>> Paul.
> >      >>>>
> >      >>>
> >      >>
> >      >
> >      
> > 
>