biopython / biopython/biopython

DSSP on Biopython

Open
#4,116 0 comments 1 reaction 1 assignee Claimed by @etal View on GitHub
Dominant language
Python
Stars
5.2k
Forks
1.9k
Avg merge
2d 6h
Merged PRs (30d)
11

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!

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.