This did the trick, Bernhard!
I replaced my coot.py file with the coot.py_0.3 file you sent, and now it starts up and all works well.
And now scheme files are loading as well. All looks good.
Many thanks for the help, all.
- Abbie -
On Sun, 9 Sep 2007, Bernhard Lohkamp wrote:
>
> 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.
>>> >>>>
>>> >>>
>>> >>
>>> >
>>>
>>>
>>
>
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