I have conducted an EM using YASARA server, and the output PDB is viewed in PyMol to understand the conformational changes between model that is energy minimized and the original model. I have used the superimpose technique to differentiate.
However , the scores I received in YASARA has got me to think on how I should Interpret. Can anyone explain how is the energy minimization of the protein should be interpreted?
Energy minimization can be a good diagnostic tool - carefully compare your initial model to the minimized one. Unusually large differences show where your original model is flawed. Try to identify and correct the problem spots in the raw model, then minimize again. Do not rely on minimization alone to fix flaws in your model, in most cases, minimization alone will not improve your model, it will just hide the flaws!
Energy minimization can be a good diagnostic tool - carefully compare your initial model to the minimized one. Unusually large differences show where your original model is flawed. Try to identify and correct the problem spots in the raw model, then minimize again. Do not rely on minimization alone to fix flaws in your model, in most cases, minimization alone will not improve your model, it will just hide the flaws!
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