Get missing terminal cappings#

Identifying missing terminal cappings in peptides and proteins.

The function molsysmt.build.get_missing_terminal_cappings() checks whether the N- or C-termini of peptide and protein chains lack terminal capping groups (such as ACE or NME) or required terminal atoms (such as OXT).

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.get_missing_terminal_cappings().

Basic usage#

Let’s show how this function works using a protein structure loaded from PDB entry 1BRS:

import molsysmt as msm

molsys = msm.convert('1BRS', selection='molecule_type=="protein"')

Now we run molsysmt.build.get_missing_terminal_cappings() to identify missing terminal groups:

missing_caps = msm.build.get_missing_terminal_cappings(molsys)

missing_caps

{412: ['OXT']}

We can select terminal oxygen atoms (OXT) using molsysmt.basic.select():

msm.select(molsys, selection='atom_name=="OXT"')

[863, 1741, 2580, 3938, 4637]