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 suggested manner(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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