I have a pdb and xplor file which contain two units of the same protein/inhibitor complex.  What I am trying to do is align the two proteins to each other so I can compare the subunits.  I can accomplish this by reading in the pdb file twice and aligning the b unit from the second pdb file to the a unit of the first pdb file.  I then split everything into objects then delete what i don't want.  In the end I have subunits a and b aligned to each other.

I would like to be able to do the same thing for the electron denisty map.  Is there a way to align maps? 

If I read in a protein and a map, then align the protein to another protein, the protein moves, but the map remains in it's original location.  Can the map coordinates be transformed somehow?

Is it possible to create some association with the protein and the map such that when the protein is aligned, the map will follow?


John Eksterowicz
Celera Genomics