This is my fault.
The problem is caused by line #5 in the /sw/bin/coot wrapper script.
Instead of
export
PYTHONPATH=/sw/lib/python2.7/site-packages:/sw/lib/python2.7/site-packages/gtk-2.0:/sw/share/coot/python:$PYTHONPATH
try
export
PYTHONPATH=/sw/lib/python2.7/site-packages:/sw/lib/python2.7/site-packages/gtk-2.0:/sw/share/coot/python
and it should work.
Coot is inheriting $PYTHONPATH from some other location, probably CCP4, and is
getting messed up. I'm about to update the fink package, as soon as I confirm
today's svn (r4386) compiles and behaves.
Sorry.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax)
email: [email protected]
On Sep 4, 2012, at 5:38 AM, Martin Montgomery <[email protected]> wrote:
>>
>> If you feel like testing, please copy over the following python files from
>> your 4303 to 4305 installation:
>>
>> python/user-defined-restraints.py
>> python/coot-utils.py
>> python/extension.py
>>
>> fingers crossed that should help.
>
> Thanks Paul,
> However, I copied over the python files from 4303 (I don't have a
> user_defined_restraints.py) and still get the error.
>
> Fatal Python error: PyThreadState_Get: no current thread
> /sw/bin/coot: line 6: 37821 Abort trap: 6 /sw/bin/coot-real "$@"
> Regards
>
> MGM
>
>
>
> On 4 Sep 2012, at 12:22, Paul Emsley <[email protected]> wrote:
>
>> On 04/09/12 10:23, Martin Montgomery wrote:
>>> Hello,
>>>
>>> I'm having trouble with 0.7-pre-1-4305 installed through fink on osx 10.8.1
>>> I updated to fink 0.34.3 then coot 0.7-pre-1-4305.
>>> Coot now crashes after the launch of the splash screen with the following
>>> message:
>>>
>>> Spacegroup: P 1
>>> Cell: 40.631 109.18 93.243 90 90 90
>>> initalize graphics molecules...done.
>>> (filter-fileselection-filenames-state)
>>> (get-active-map-drag-flag)
>>> (use-graphics-interface-state)
>>> DEBUG:: stating pydirectory /sw/share/coot/python
>>> INFO:: importing coot.py from /sw/share/coot/python/coot.py
>>> Importing python module coot using command from coot import *
>>> INFO:: coot.py imported
>>> Fatal Python error: PyThreadState_Get: no current thread
>>> /sw/bin/coot: line 6: 50934 Abort trap: 6 /sw/bin/coot-real "$@"
>>>
>>> The previous version (4303) was working perfectly (and still is on my
>>> laptop with fink 0.34.2).
>>>
>>> A quick google showed at least two others had found the same problem but
>>> hadn't posted to the list.
>>>
>>> Is there a fix?
>>>
>>>
>>
>> I didn't know about this recent problem until I (too) did some googling.
>>
>> I did see a ChangeLog entry from 2004:
>>
>> * src/main.cc (main): Put PYTHON macroed code before GUILE, so
>> that python is initialized when we have --with-guile
>> --with-python, which deals with "Fatal Python error:
>> PyThreadState_Get: no current thread".
>>
>>
>> which makes me believe that I have inadvertently somehow made a similar
>> mistake (that is only apparent on Mac XXX). How I could have done that and
>> why it only fails on Mac, I don't know.
>>
>> Having said that, if you have localized the problem between 4303 and 4305
>> (as seems to be the case), Bernhard (who is now on holiday) wrote r4304 and
>> r4305 - but that consists mostly of python scripting changes (the prosmart
>> interface, in particular).
>>
>> If you feel like testing, please copy over the following python files from
>> your 4303 to 4305 installation:
>>
>> python/user-defined-restraints.py
>> python/coot-utils.py
>> python/extension.py
>>
>> fingers crossed that should help.
>>
>> Paul.
>>
>>
>>
