Path B - Module 26: Attribute Engineering (Patching)#

A clean model is a professional model. When you merge different components (like your enzyme and the His-tag), the resulting chain IDs and entity names might be messy.

In this module, you will learn to use set() to “patch” your industrial biocatalyst and make it ready for a high-quality technical report.

import molsysmt as msm
from molsysmt import systems

# Load the system we built in the previous module (Enzyme + Tag)
petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')
his_tag = msm.build.build_peptide('HHHHHH')
system = msm.merge([petase, his_tag])

1. Renaming the Catalyst Chain#

By default, the enzyme might have chain ID “A”. Let’s rename it to “ENZ” to indicate it is the main catalyst.

# Identify the first chain (the enzyme)
msm.set(system, element='chain', selection='chain_index==0', 
        chain_name='CATALYST', chain_id='E')

msm.info(system, element='chain')

2. Patching the Purification Tag#

The 6xHis-Tag we merged is now the second chain. Let’s give it a clear name so everyone in the pipeline knows what it is.

# Rename the second chain
msm.set(system, element='chain', selection='chain_index==1', 
        chain_name='HIS_TAG', chain_id='T')

msm.info(system, element='chain')

3. Entity Identity#

Let’s update the entity names. This is the highest level of hierarchy and it is what appears in the system summary.

# Update entity names
msm.set(system, element='entity', selection='name=="AMYLOID-BETA PROTEIN"', name='Engineered PETase')
msm.set(system, element='entity', selection='name=="POLY-HISTIDINE"', name='Purification Tag')

msm.info(system, element='entity')

🏆 Path B Challenge: The Data Polisher#

  1. Use msm.set() to change the Atom Names of the His-tag from “CA” to “CALPHA” (just as a test of mass patching).

  2. Rename all the Water residues to “SOL” (Solvent).

  3. Verify that your system now has two entities with the names: “Engineered PETase” and “Purification Tag”.

  4. Check the total number of atoms in the system after your patches.

Your model is now perfectly documented. In Module 27, we will learn how to change the Conformation of a key residue in the active site.