Vadim Patsalo wrote:
The model with the lower DOPE score is better. You should also evaluate the _template_ with the DOPE score -- you can find a script to do this in examples/commands/assess_dope.py. This will give you an idea of how the model compares with your template.
There is very little value in comparing the model with the template, since by construction it should look similar. Plus, DOPE scores are not normalized, so you cannot compare them for different structures. One thing you can do is plot DOPE profiles for both template and model and compare them by eye, as this gives you a rough idea whether your alignment is correct. See the end of the basic tutorial on the Modeller website for an example.
Ben Webb, Modeller Caretaker
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