[Biopython] Problem when adding a residue

[Claudia Millán Nebot]

Hi Lenna,

thanks for the quick answer. It makes perfect sense and now is working.

Best,

Claudia

2016-07-25 14:08 GMT+01:00 Lenna Peterson <arklenna at gmail.com>:

> Hi Claudia,
>
> Rather than add the residue directly to the structure, you need to add it
> to a chain. So you will want to do something like
> `structure[0]["A"].add(...)` (depending on the models/chains in your
> structure).
>
> The PDB object in Biopython has 5 hierarchical levels:
> Structure
> Model
> Chain
> Residue
> Atom
>
> The error occurred because the `PDBIO.save` method expects the child of a
> `Structure` object to be a `Model` object, which has the attribute
> `serial_num`.
>
> Let me know if you still run into any problems.
>
> Cheers,
>
> Lenna
>
> On Mon, Jul 25, 2016 at 7:26 AM, Claudia Millán Nebot <cmncri at ibmb.csic.es
> > wrote:
>
>> Dear all,
>>
>> I am using Biopython to parse a pdb model extracted from a larger pdb and
>> if a condition is met, complete it with some residues from the original pdb
>> model. The residue object that I am trying to add was saved when parsing
>> the original larger pdb, but when I am trying to add it to the new model I
>> am getting this error:
>>
>>   File
>> "/Library/Python/2.7/site-packages/biopython-1.66-py2.7-macosx-10.11-intel.egg/Bio/PDB/PDBIO.py",
>> line 187, in save
>>
>>     fp.write("MODEL      %s\n" % model.serial_num)
>>
>> AttributeError: 'Residue' object has no attribute 'serial_num'
>>
>>
>> The pdb model that I am completing might have some changes in the chain
>> nomenclature, could that be the reason for the error? But apparently is
>> raised for something related with the model... so I am not sure what is
>> happening.
>>
>> This is the relevant piece of code where the error happens:
>>
>>                         if add==True and checkres!=resi.get_full_id()[-1
>> ]:
>>
>>                               ncheckres=checkres[1]
>>
>>                               print "Adding ncheckres",ncheckres
>>
>>                               print
>> "dictio_template[ncheckres]['residue_object']"
>> ,dictio_template[ncheckres]['residue_object']
>>
>>                               checkresobj=dictio_template[ncheckres][
>> 'residue_object']
>>
>>                               #print "resi.serial_num",resi.serial_num()
>>
>>                               #print
>> "list_res[i+1].serial_num",list_res[i+1].serial_num()
>>
>>                               #print
>> "checkresobj.serial_num",checkresobj.serial_num()
>>
>>                               structure.add(dictio_template[ncheckres][
>> 'residue_object'])
>>
>> Thanks in advance,
>>
>>
>> Claudia
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>
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