[BioPython] Using Bio.PDB to add atoms to a structure?
Konrad Forster Koehler
konrad.koehler at mac.com
Mon Oct 23 16:32:09 UTC 2006
Using Bio.PDB, I was wondering if there is a way to:
1) read in a structure from a PDB file
2) calculate the position of a new chain/residue/atom
3) add new these chains/residues/atoms to the structure
4) write of the PDB file containing the original + new atoms
I have no problem with steps 1, 2, and 4, but I am stuck on step #3.
I have tried things like:
http://bioinformatics.org/bradstuff/bp/api/Bio/PDB/StructureBuilder_StructureBuilder.py.html#init_chain
builder = StructureBuilder()
chain_x = builder.init_chain("0","X")
error message: init_chain() takes exactly 2 arguments (3 given)
or
chain_x = builder.init_chain("X")
error message: StructureBuilder instance has no attribute 'model'
I have googled for examples or documentation on adding new atoms using Bio.PDB, but I have not found anything.
Can anyone provide me with any pointers, examples, etc?
Best regards,
Konrad
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