Introduction

In PDB files, not all the atoms locations of a biological assembly and the crystallographic asymmetric unit are given. The transformations information, rotational and translational (for both crystallographic and non-crystallographic), needed to reconstruct the multimer, is given in REMARK 350 and MTRIX line of the pdb file.

Phenix provide a commands to create a pdb file of the reconstructed a multimer for both the biological assembly and the crystallographic asymmetric unit.

The bioassembly_reconstruction command function applies all the transformations in the the pdb file REMARK 350 BIOMT, to each of the chains, produces new chains with new coordinates and adds them to the current model. The crystall_asym_unit_reconstruction does the same, using the MTRIX data.

Command-line use

Usage: phenix.pdb.biomt_reconstruction [pdf_file] [pdf_file] [options]

Options:
  --help, -h

Example:

  >>> phenix.pdb.biomt_reconstruction 'input_file_name.pdb'
  bio-assembly reconstructed pdb file was added to your current directory
  /path/biological_assembly_input_input_file_name.pdb

   >>> phenix.pdb.biomt_reconstruction 'input_file_name.pdb' 'output_file_name.pdb'
  bio-assembly reconstructed pdb file was added to your current directory
  /path/output_file_name.pdb

Usage: phenix.pdb.mtrix_reconstruction [pdf_file] [pdf_file] [options]

Options:
  --help, -h

Example:

  >>> phenix.pdb.mtrix_reconstruction 'input_file_name.pdb'
  bio-assembly reconstructed pdb file was added to your current directory
  /path/crystall_asymmetric_unit_input_file_name.pdb

   >>> phenix.pdb.mtrix_reconstruction 'input_file_name.pdb' 'output_file_name.pdb'
  bio-assembly reconstructed pdb file was added to your current directory
  /path/output_file_name.pdb

Output

For both commands the output is a pdb file in the current working directory