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I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?structureId=2PJY.

How can I generate the PDB for the full dimer?

I am comfortable with PyMol, so an answer using PyMol is preferred.

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  • $\begingroup$ Use SymmDock. It is very easy. $\endgroup$ – Laura LINDO Nov 15 '18 at 16:40
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This article will probably be informative for you: Looking at Structures: Introduction to Biological Assemblies and the PDB Archive

The PDB file contains the asymmetric unit found in a particular crystallographic study. The biological assembly is the quaternary structure known or predicted to be found in living systems. For many proteins (but not 2PJY), the biological assembly can be downloaded directly from RCSB. For other proteins, the PDB file may contain the transformation matrix used to create the biological assembly from the asymmetric unit. If you look at the file in a text editor, this information is found under remark 350:

REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 8880 ANGSTROM**2                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C                               
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   2  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000    

Note that the actual biological assembly of 2PJY is a hexamer and the asymmetric unit in the PDB file is a trimer. You can see that the first matrix is identity (ie keeps the original asymmetric unit). The second matrix transforms the assymmetric unit to create the full hexamer. This matrix is both author and PISA predicted. You can actually go to the PISA website and have it predict the biological assembly of a particular PDB file, and it will spit out the coordinates of the hexamer (and other predicted assemblies) which you can then load into PyMOL.

PDB files may also contain a CRYST1 record, which gives information about the unit cell and space group of the crystal. Via the symexp command, PyMOL can use this information to recreate neighboring asymmetric units. By limiting the cut-off distance (and this requires trial-and-error), the biological assembly can be recreated. This script, for example, will generate the hexamer:

fetch 2PJY
symexp 2PJY, 2PJY, 2PJY, 2.5
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