Make bioassembly#

Constructing biological assemblies using symmetry transformations from PDB records.

Biological assemblies (or biomolecules) represent the functional quaternary structure of a macromolecule, often generated by applying crystallographic symmetry operations to the asymmetric unit. The function molsysmt.build.make_bioassembly() constructs a full biological assembly from PDB or mmCIF records.

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.make_bioassembly().

Basic usage#

Let’s show how to construct a biological assembly from PDB entry 1OUT:

import molsysmt as msm

molsys = msm.convert('1OUT')

msm.view(molsys)

Now we apply symmetry operations to construct biological assembly '1':

molsys = msm.build.make_bioassembly(molsys, bioassembly='1')

msm.view(molsys)

Let’s look at a second example using PDB entry 2BUK:

molsys = msm.convert('2BUK')

msm.view(molsys)

We construct biological assembly '1' for 2BUK and inspect its summary. Each generated chain receives a unique chain_id: source identifiers are preserved once, and collisions continue with uppercase labels (A through Z, then AA, AB, and so on). The author-provided chain_name remains unchanged and may therefore repeat across copies:

assembled_molsys = msm.build.make_bioassembly(molsys, bioassembly='1')

msm.info(assembled_molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_ions	n_proteins	n_structures
molsysmt.MolSys	95280	20700	9720	300	9720	180	9480	180	60	1

msm.view(assembled_molsys)