how to download interface generated with PDBe PISA?

Question

[Hydrogen Bond]

I have a list of monomers, only one chain in the asymmetric unit of PBD entry. I want to generate crystal interface for these monomers using PISA server. I can do it online and download manually the interface with the larget area. How to do it via command line terminal?

[Hydrogen Bond]

https://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver

Answer 1

[Wayne]

Someone posted a similar question shortly before this one over at Stackoverflow. If you need to do a lot and like Python, I've written a script I describe in this post. The examples have using Snakemake to run it in pipeline to get a lot of them from a list of PDB codes.

The underlying tech uses that link you posted about for retrieval. But I made it easy to get a nicely formatted Pandas dataframe from them. Since it is Python code based it can more easily be used for downstream analysis.

The script will also take the text that can be copied from the interface page as a way to allow that route. This route also allows editing the file if you have an interface report list that my script has a particularly hard time processing correctly.

Direct links:

• script pisa_interface_list_to_df.py and description
• a series of Jupyter notebooks served in active form via MyBinder