[Biojava-l] Partial ORGANISM_SCIENTIFIC name returned from PDB 4xcw

[Jose Manuel Duarte]

I forgot to mention, the mmCIF parser is fine with this and returns the 
correct organism string.

So the other solution is simply to use mmCIF files. To load a structure 
from mmCIF with AtomCache you need something like this:

     AtomCache cache = new AtomCache();
     StructureIO.setAtomCache(cache);
     cache.setUseMmCif(true);

     Structure struct = StructureIO.getStructure("4XCW");

In general it is a good idea to use mmCIF, since they have more complete 
and better structured information. Additionally, the PDB has already 
stopped providing some large structures in the PDB format, so the only 
way to cover the whole PDB is to use mmCIF.

Good luck

Jose



On 25.06.2015 17:16, Jose Manuel Duarte wrote:
> Hi Guoying
>
> Thanks for reporting the problem. I've added the issue to github and 
> fixed it:
>
> https://github.com/biojava/biojava/issues/289
>
> The next release of biojava should then contain the fix.
>
> Note that you can also directly open issues in github to report 
> specific problems like this one.
>
> Cheers
>
> Jose
>
>
> On 25.06.2015 15:38, Guoying Qi wrote:
>> For PDB 4xcw, only partial organism scientific name returned by the 
>> following method:
>>
>> getOrganismScientific()
>> org.biojava.nbio.structure.Compound
>>
>> HELICOBACTER PYLORI (STRAIN J99 / ATCC 7
>>
>> I traced back to PDBFileParser,  it seems this PDB file being treated 
>> in legacy format and the line length being trimmed into 72.
>>
>> Can this problem be fixed somehow?
>>
>> Thanks.
>>
>> Guoying Qi
>>
>>
>> _______________________________________________
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>
>
>
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