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+# Geometry Optimization using RosettaQM
+
+## Summary
+In this tutorial, we are going to give an example of geometry optimization for a protein.
+
+## Tutorial
+In this case, we have part of a zinc-finger protein. We want to optimize the geometry of protein:
+* in proximity of zinc, with quantum mechanics,
+* its neighbourhood with a lower level of theory quantum mechanics,
+* and the rest of protein with Rosetta's energy field.
+
+
+
+Figure 1.
+
+
+Therefore, the protein will be seperated into three regions, which will be called reg1, reg2 and reg3, respectively. Then, different movers and scorings will be applied for each reigon.
+
+Residue selectors ae used to specify each region.`reg1` is selected by residue numbers, and `reg2` is selected by `Neighborhood` selector. This selector compares the distance between beta carbons of selection (in this case, `reg1`) with beta carbons of other residues. If the distance is less than or equal to the threshold (in this case, 4A) it selects that residue. The `include_focus_in_subset="false"` tag means `reg2` excludes `reg1`. Figure 2. highights `reg1` with dark blue, and `reg2` with light blue. `reg3` is selected as anything not in `reg1` or `reg2` regions.
+
+```
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+
+
+```
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+Figure 2.
+
+
+For each region, a different score function needs to be used. The following table gives a summary of that.
+
+| Region's name | Score function |
+|-------------|----------------|
+| reg1 | |
+| reg2 | AM1. a semi-empirical score function|
+| reg3 | Rosetta ref2015 |
+
+
+```
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+```
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+```
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+```
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