Get missing residues#

Identifying missing amino acid or nucleotide residues in a molecular system.

Experimental structures often omit flexible loops or terminal residues due to unresolved electron density. The function molsysmt.build.get_missing_residues() compares resolved residues against reference sequence records (such as _entity_poly_seq in mmCIF or SEQRES in PDB files) to identify missing residues.

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_residues().

Basic usage#

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

import molsysmt as msm

First, we convert PDB entry 1BRS into a standard molsysmt.MolSys object:

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

Let’s inspect the protein molecules in the system:

msm.info(molsys, element='molecule')

index	name	type	n atoms	n groups	n components	chain index	entity index	entity name
0	BARNASE	protein	864	108	1	0	0	BARNASE
1	BARNASE	protein	878	110	1	1	0	BARNASE
2	BARNASE	protein	839	108	1	2	0	BARNASE
3	BARSTAR	protein	693	87	2	3	1	BARSTAR
4	BARSTAR	protein	665	86	2	4	1	BARSTAR
5	BARSTAR	protein	699	89	1	5	1	BARSTAR

Now we call molsysmt.build.get_missing_residues() using the PDB identifier '1BRS' to compare the resolved residues against the reference sequence records:

missing_residues = msm.build.get_missing_residues('1BRS')

missing_residues

{(0, 0): ['ALA', 'GLN'],
 (2, 0): ['ALA', 'GLN'],
 (3, 63): ['GLU', 'ASN'],
 (4, 0): ['LYS'],
 (4, 62): ['GLU', 'ASN']}