biopython / biopython/biopython
DSSP on Biopython
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Description
### Setup
I am reporting a problem with Biopython 1.76, Python 3.10, and operating
system Ubuntu 16.04
```python
from Bio.PDB.DSSP import DSSP
parser = PDB.PDBParser()
struct = parser.get_structure("1a2y", "1a2y.pdb")
model = struct[0]
dssp = DSSP(model, "1a2y.pdb", dssp="mkdssp", acc_array="Miller")
print(dssp.property_dict)
```
### Question
Hi,
I have two questions.
It is my understanding that in the `DSSP` class `mkdssp` is run on the PDB file specified by the `in_file` argument, and the code above works fine for me. But,
1. Why do we also have to input a `Bio.PDB.Model.Model` instance for the `model` argument? Isn't a PDB file sufficient for a DSSP excutable?
2. Is there a way to specifying the chains to be processed by the DSSP executable? E.g., In `1a2y.pdb` it is an antibody-antigen complex with A and B as two antibody (Ab) chains and C as the antigen (Ag) chain. If I want to run DSSP on the Ab chains and the Ag chain respectively, how could I do that?
Thanks for your time!
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