[Chimera-users] After fitting a PDB into a cryo-EM density, is it possible to color the PDB atoms by the local EM density in the cryo-EM map?

Lai, Jonathan jlai7 at illinois.edu
Tue May 27 14:53:26 PDT 2014

Dear Chimera-users,

I have several cryo-EM maps of an assembly process and a PDB of the final product; what I want to do is to have a visual depiction of how the local EM density around structural elements in the final product changes over time.   After fitting the PDB into the cryo-EM density, I am wondering if it is possible to color the PDB atoms by a reference EM density at each point.  For example, I want to color every residue that intersects isosurface == 0 blue, every residue that intersects isosurface == 1 red, and have a continuous color scheme for all intermediate values from (0 to 1).  I already have fitted the PDBs into the cryo-EM maps.  Is there any easy way to do this?

Jonathan Lai
University of Illinois at Urbana-Champaign
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