Building biological assembly and crystallographic asymmetric unit from a PDB file
- Introduction
- Command-line use
- Biological Assembly
- Crystallographic Asymmetric Unit
- Output
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
Biological Assembly
Usage: phenix.pdb.bioassembly_reconstruction [pdf_file] [pdf_file] [options]
Options:
--help, -h
Example:
>>> phenix.pdb.bioassembly_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.bioassembly_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
Crystallographic Asymmetric Unit
Usage: phenix.pdb.bioassembly_reconstruction [pdf_file] [pdf_file] [options]
Options:
--help, -h
Example:
>>> phenix.pdb.crystall_asym_unit_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.crystall_asym_unit_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
| 