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ProLint / prolintpy

A python package for the automated analysis and visualization of lipid-protein interactions.
https://prolint.github.io/prolintpy
MIT License
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Using Prolint for Lipid Analysis #5

Closed RayHackett closed 2 years ago

RayHackett commented 2 years ago

I was wondering how to apply Prolint to an atomistic trajectory of a protein with a ligand. The Tutorial indicates this is possible: https://prolint.github.io/prolintpy/#/ligands

I've tried loading my ligand (named 'LIG' in the topology) as a lipid with:

lipids = pl.Lipids(t.topology, resolution='atomistic', lipid_names=['LIG'])

This seems to work:

lipids.lipid_count() {'LIG': 1}

However, running contacts.compute_neighbors gives: KeyError: 'LIG'

contacts = pl.ComputeContacts(t, proteins, lipids) result = contacts.compute_neighbors(t, cutoff=0.5)

The full error message is attached.

What is the correct/intented way to load a ligand with Prolint? lig_error.txt

bisejdiu commented 2 years ago

compute_neighbors takes a grouped argument which is by default set to True and that will do a lipid lookup (e.g. it groups POPCs lipid into PC category). Your ligand is not recognized as part of the lipid library, hence the error. If you set grouped=False, it should fix this.

Have a look at this #4

RayHackett commented 2 years ago

Fantastic! Thank you!