Hi Ian,
This is bizarre, we also have 6.1.13 installed here, but in my ADN.cif
(dated Oct 29 2008) the atom names have primes, but are surrounded by
quotes which I think allows a mechanism for them to be converted to a
* if you have the appropriate changes listed in your (personal) library.
I don't understand why these differ (unless Phil change the ADN.cif
entry here for some reason).
I think we need a comment for the library people !
Cheers
Andrew
On 15 Mar 2011, at 14:23, Ian Clifton wrote:
> On 15/03/11 12:57, A Leslie wrote:
> …
>>
>> I then try using LIBCHECK standalone to get the PDB file. I get the
>> same error if I use the FILE_CIF input keyword and give it the
>> filename for ADN.cif, no surprise, as this is (I assume) what COOT
>> does.
>>
>> I then copy over ADN.cif to my local directory, run LIBCHECK again
>> and
>> use the FILE_L keyword to specify the (local) ADN.cif file. I then
>> get
>> the error:
>>
>> ERR: item _chem_comp_tree.atom_id :O2' not found in the atom list
>> MON,BLOCK :ADN data_comp_ADN
>>
>> suggesting that there is an error in ADN.cif !
>>
>
> I can’t reproduce this (CCP4-6.1.13), but I’m immediately suspicious
> of
> the apostrophe (U+0027) character in the error message. I’m not a DNA
> dabbler, so I can’t help much, but I bet the problem is due to
> “primed”
> atom names being replaced by stars, or something else. In my CCP4
> distribution, the atom names are starred in the dictionary file for
> ADN.
> In official PDB files, they’re primed I think.
> --
> Best wishes,
> Ian.
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