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
>>>>
>>>
>>
>
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