Individual collation

Individual collation#

In this tutorial, we introduce tmkit.collate, a module designed to collate a protein chain downloaded from PDBTM by comparing it with chains of the same protein from RCSB.

Tip

Collation is often necessary when working with PDBTM-derived protein chains, as PDBTM may transform or exclude certain chains present in the RCSB PDB structure file.

This tutorial provides a step-by-step example of how to detect and analyze these differences at the per-protein level.

Reminder of data

Please make sure that the build-in example dataset has been downloaded before you walk through the tutorial.

Example usage#

First, we need to prepare RCSB and PDBTM structures of proteins. We have put a few protein structures in the following folders if you have downloaded our example dataset. Alternatively, you can obtain them through this tutorial.

pdb_rcsb_fp = 'data/pdb/collate/rcsb/'
pdb_pdbtm_fp = 'data/pdb/collate/pdbtm/'

Then, we can check how many chains there are and what chains are contained in there by using the following code.

import tmkit as tmk

# PDBTM
chains = tmk.collate.chain(
    prot_name='6cxh',
    pdb_fp=pdb_pdbtm_fp,
)
print(chains)

# output
======>protein has chains ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']

If we focus on a certain chain C of protein 6cxh, we can get how many other chains differ to each other or are the same. The output dataframe allows you to see there are chains GDEHF from RCSB that are different from those from PDBTM. The transformation_detection is used to check if the chain of focus is transformed by another chain from a RCSB PDB structure. untransformed means it is not transformed by another chain. Please see the output below.

import tmkit as tmk

df, transformation_detection = tmk.collate.single(
    prot_name='6cxh',
    chain_focus='C',
    pdb_rcsb_fp=pdb_rcsb_fp,
    pdb_pdbtm_fp=pdb_pdbtm_fp,
)

# output
print(df)
prot_name chain pdbtm_chains rcsb_chains source   diff same
0      6cxh     C     ABCDEFGH         ABC   rcsb  GDEHF  ACB

print(transformation_detection)
{'6cxh.C': 'untransformed'}

If we test protein 3pux chain G, we found that the PDB structure from PDBTM is the same as that from RCSB, shown below.

import tmkit as tmk

df, transformation_detection = tmk.collate.single(
    prot_name='3pux',
    chain_focus='G',
    pdb_rcsb_fp=pdb_rcsb_fp,
    pdb_pdbtm_fp=pdb_pdbtm_fp,
)

# output
print(df)
  prot_name chain pdbtm_chains rcsb_chains source diff   same
0      3pux     G        EFGAB       EFGAB   rcsb       AEFGB

print(transformation_detection)
{'3pux.G': 'untransformed'}

Attributes#

Attribute

Description

prot_name

name of a protein in the prefix of a PDB file name (e.g., 1xqf in 1xqfA.pdb)

chain_focus

chain of a protein in the prefix of a PDB file name (e.g., A in 1xqfA.pdb)

pdb_rcsb_fp

path to a protein complex from RCSB

pdb_pdbtm_fp

path to a protein complex from PDBTM

See also

Please see here for better understanding the file-naming system.

Output#

======>protein has chains ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']
======>basic info:
  prot_name chain pdbtm_chains rcsb_chains source diff   same
0      3pux     G        EFGAB       EFGAB   rcsb       AEFGB
  prot_name chain pdbtm_chains rcsb_chains source diff   same
0      3pux     G        EFGAB       EFGAB   rcsb       AEFGB
{'3pux.G': 'untransformed'}
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