[Biopython] Problem when adding a residue
Claudia Millán Nebot
cmncri at ibmb.csic.es
Mon Jul 25 11:26:25 UTC 2016
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
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