Triply puzzled now! Something weird must be going on somewhere under the
hood (bonnet), to make this sometimes cause an error and sometimes not.
Wayne
On Mon, 8 Nov 2010, Richard Harris wrote:
> Hi Wayne
>
> Okay here are the results:
>
>>>> p = top.project
>>>> c = p.findFirstChemCompCoord(ccpCode='Atp')
>>>> c.isModified
> False
>
> added in sequence (MSL)
>
>>>> c.isModified
> False
>>>> start generating output : ccp.nmr.Nmr.NmrProject
> start generating output : ccpnmr.Analysis.AnalysisProject
> start generating output : ccp.molecule.Molecule.Molecule
> start generating output : ccp.molecule.MolSystem.MolSystem
> successfully saved project
>
> So this works!?!
> There are no .bak files in the
> /usr/local/ccpnmr/ccpnmr2.1/data/ccp/molecule/ChemCompCoord directory
>
> thanks
> Richard
>
>
>> Definitely curious. I can't reproduce this but it's likely I'm not doing
>> the same things. So can you try the following at the Python prompt before
>> you add the sequence:
>>
>>>>> p = top.project
>>>>> c = p.findFirstChemCompCoord(ccpCode='Atp')
>>>>> c.isModified
>>
>> You should get False as the result. Then add the sequence. And again
>> check:
>>
>>>>> c.isModified
>>
>> I assume it now says True. But if it still says False and you do a save
>> then presumably the save will fail again. If it says False then the save
>> should not be trying to save the Atp ChemCompCords (because it is not
>> modified) but it seems that it is trying to save it. If it says True then
>> there's definitely some bug in the code that is adding the sequence (or
>> related code).
>>
>> I just had a thought. Are there any *.bak files pre-existing in the
>> /usr/local/ccpnmr/ccpnmr2.1/data/ccp/molecule/ChemCompCoord directory?
>> (In particular one for Atp.) If so the solution might just be to delete
>> those *.bak files (or gzip tar them up and put that in some other
>> directory).
>>
>> Wayne
>>
>> On Mon, 8 Nov 2010, Richard Harris wrote:
>>
>>> Hi
>>>
>>> No the sequence was just standard amino acids - then I just tried with
>>> the
>>> amino acids MSL as the sequence and still got the error on saving.
>>> Yes /usr/local is root access only.
>>>
>>> Richard
>>>
>>>> Hello,
>>>>
>>>> This is puzzling. I don't know why in the world it would ever try to
>>>> be
>>>> backing up the Atp ChemCompCoord (which are the default coordinates for
>>>> Atp), since that is reference data. I've forwarded to Tim and Rasmus
>>>> in
>>>> case they have any ideas. Did the sequence you add include Atp? Or
>>>> did
>>>> it include some component that needed to be downloaded over the web?
>>>> Or
>>>> was it just bog standard? Now /usr/local is presumably root write
>>>> access
>>>> only so once it decided to try and back Atp up that would cause the
>>>> error.
>>>>
>>>> Wayne
>>>>
>>>> On Mon, 8 Nov 2010, Richard Harris wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> I have a newly installed version of 2.1.5 from the analysis
>>>>> pre-compiled
>>>>> binaries and have freshly updated it.
>>>>> I can save a project until I add in a sequence and then I get a pop up
>>>>> window with:
>>>>>
>>>>> [Errno 13] Permission denied:
>>>>> '/usr/local/ccpnmr/ccpnmr2.1/data/ccp/molecule/ChemCompCoord/pdb+other+Atp+msd_ccpnRef_2008-08-04-14-06-41-501_00001.xml.bak'
>>>>>
>>>>> have checked the permissions in the directory and compared to another
>>>>> installation and they appear to be the same.
>>>>>
>>>>> any ideas?
>>>>>
>>>>> thanks
>>>>> Richard
>>>>>
>>>>
>>>
>>
>
|