[Chimera-users] Matrix Application

Amanda Constantinides aconstantinides1 at student.gsu.edu
Mon Oct 23 10:05:38 PDT 2017

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want to superpose the N-terminal subunits (A), note the RMSD, then apply the resulting matrix to the superposition of both subunits of the molecule with both subunits of the other (B),then I want to superpose on the C-terminal subunits (C), and then measure the RMSD between (C) and the C-terminal subunits from (B). How can I do this in Chimera? I know how to superpose molecules and calculate the RMSD in Chimera, but I do not know how to apply the resulting matrix from (A) to (B). I tried to save the aligned structures from (A) as a PDB file to check and see if there was a matrix in the file, but an error message came up saying that I needed to save the file as $name or $number. I tried to save the file with $ in front of the name, but it didn't work.

Thanks in advance,

Amanda Constantinides

Graduate Research Assistant
Georgia State University
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