We discovered the problem: the file $CBIN/buccaneer_pipeline needs to
be told to expand its lookup path, so we inserted in the 2nd line:
sys.path.append("/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/")
We had this fix in our previous installation as well, but can't remember
where we got it from; I have no idea why only we seem to need it (is
nobody else running buccaneer? Then they're fools: it's massively
useful...)
Cheers
phx
On 18/10/2011 10:52, Tim Gruene wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> And you do have read access to
> /usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/CCP4pipeline.py
> (on our installation, the mode is actually 755, but I suppose 644 should
> be sufficient).
> You can set PYTHONVERBOSE to 1 or higher in the shell you start ccp4i
> from to see what python is doing ('man python').
>
> Tim
>
> On 10/18/2011 11:34 AM, Frank von Delft wrote:
>> Mine reads:
>> /usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python:/usr/local/ccpnmr/ccpnmr1.0/python
>>
>>
>> That should work, right? Where else can I look, for the failing
>> import? This is a lettuce-fresh install, pulled straight off web and
>> installed with all defaults.
>>
>> Cheers
>> phx.
>>
>>
>> On 18/10/2011 08:38, Tim Gruene wrote:
>> Hi Frank,
>>
>> it may not be the python binary itself but the PYTHONPATH which is
>> incorrectly set. After initialising ccp4, mine reads
>> tg@slartibartfast:~$ echo $PYTHONPATH
>> /xtal/Suites/CCP4/ccp4-6.2.0/share/python:
>> which is modified around line 231 in $CBIN/include/ccp4.setup
>>
>> My python binary is /usr/bin/python, and I have used buccaneer without
>> errors.
>>
>> Tim
>>
>>
>>
>> On 10/17/2011 09:30 PM, Frank von Delft wrote:
>>>>> Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer
>>>>> fails from the GUI. Below is what shows up if you view the com file
>>>>> before execution; and below that the logfile.
>>>>>
>>>>> Seems to me it's using the wrong python executable; the first one on my
>>>>> path is certainly nothing to do with ccp4, so now wonder it can't
>>>>> import.
>>>>>
>>>>> Shouldn't python be invoked explicitly with its full path? Where can I
>>>>> set this? (Mind you, setting it in the Run&View didn't work.)
>>>>> Cheers
>>>>> phx
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *Run&View Com File: *
>>>>> python -u /usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin
>>>>>
>>>>>
>>>>> *Logfile*
>>>>> #CCP4I VERSION CCP4Interface 2.1.0
>>>>> #CCP4I SCRIPT LOG buccaneer_pipeline
>>>>> #CCP4I DATE 17 Oct 2011 18:45:20
>>>>> #CCP4I USER loretta
>>>>> #CCP4I PROJECT PROJECT
>>>>> #CCP4I JOB_ID 13
>>>>> #CCP4I SCRATCH /tmp/loretta
>>>>> #CCP4I HOSTNAME hestia.sgc.ox.ac.uk
>>>>> #CCP4I PID 13684
>>>>>
>>>>> ***************************************************************************
>>>>>
>>>>> * Information from CCP4Interface script
>>>>> ***************************************************************************
>>>>>
>>>>> The program run with command: python -u
>>>>> /usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin
>>>>> has failed with error message
>>>>> Traceback (most recent call last):
>>>>> File "/usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline", line
>>>>> 3, in<module>
>>>>> from CCP4pipeline import Control
>>>>> ImportError: No module named CCP4pipeline
>>>>> ***************************************************************************
>>>>>
>>>>>
>>>>>
>> -- - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
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