Dear all, I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure. I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue. Thanks, Joydeep.
Dear Joydeep, When you first open structures, Chimera just uses the x,y,z coordinates in the input files; it does not automatically superimpose (overlay) similar structures. Although the structures look almost superimposed, they could probably be superimposed better, so you could try doing that with the Matchmaker tool (menu: Tools… Structure Comparison… Matchmaker). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> Different ways to superimpose structures in Chimera are listed here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> See also the tutorials, for example “Superpositions and Alignments”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2019, at 8:24 AM, Chakraborty, Joydeep <jc323@njit.edu> wrote:
Dear all, I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure. I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue. Thanks, Joydeep. <MS Actv site pocket.pptx>
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Chakraborty, Joydeep -
Elaine Meng