[Chimera-users] Biological dimer shows up as a monomer

Tom Goddard goddard at sonic.net
Mon Jun 13 11:13:24 PDT 2011

Hi Jim,

   The 2rgr PDB file contains just the monomer atomic coordinates.  You 
can get the dimer by opening it in Chimera then use Model Panel 
(Favorites menu) and press the Biological Unit button.  This uses the 
REMARK 350 biological unit matrices in the PDB file to create the dimer.


> I'm new to Chimera and trying to create a figure panel for a paper.
> I'm running Chimera on a Mac from the graphical interface.
> The protein is a a yeast topoisomerase II.  Its PDB ID is 2RGR.
> If I view the protein with Cn3D I can see the whole biological unit,
> in which the protein is present as a symmetrical dimer (with some DNA
> strands too).  If I view it with Chimera I see a protein monomer.  The
> problem is I want to illustrate a particular intermolecular salt
> bridge, which is present in the dimer but isn't present in the monomer.
> Is there some preference to toggle to allow Chimera to display the
> whole biological unit?  Or would I have to artificially build a dimer
> out of two monomer models?
> Thanks,
> Jim
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> James E. Ferrell, Jr., M.D., Ph.D.
> Professor and Chair of Chemical and Systems Biology
> Stanford University School of Medicine
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