[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]

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?

Cheers,
Jonathan Lai
University of Illinois at Urbana-Champaign
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140527/1a0c5c20/attachment.html>