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Add minor tweaks to the Cryo-EM tutorial
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pemsley committed May 20, 2024
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13 changes: 3 additions & 10 deletions blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md
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Expand Up @@ -42,17 +42,11 @@ You should now see a map with three unfitted parts

![Moorhen 3 Domains]({{"../../../images/moorhen-3-domains.png"}})

Let's fit the nanobody!

### Fitting the Nanobody

Now we want to model the nanobody domain.

We have done a BLAST search for the sequence of our nanobody and know that the structure was published already in a different complex - it's the "E" chain in the entry ``6GDG``. So let's fetch that structure, extract the "E" chain and then fit it to our reconstruction.

- First centre the view on the centre of the nanobody/immunoglobulin domain.


Fetch the Reference Structure:

- **File** → **Fetch from Online Services** → `6gdg`
Expand All @@ -66,7 +60,8 @@ Now make the fragment we need from that:

So now we have the "E" chain floating around in space...

- Delete the `6gdg` model
Delete the `6gdg` model:

- **Models** Click on the gear icon of the `6gdg` molecule and **Delete molecule**

Change the representation of the '//E' chain
Expand Down Expand Up @@ -113,10 +108,8 @@ To refine this domain/chain:
- Atom Selection is `//` (i.e. "all atoms")
- **OK**



You will see that the nanobody is now highlighted with green bonds and atoms.
A dialog will appear middle top
A dialog will appear at the middle top

![Moorhen Selection Panel]({{"../../../images/moorhen-selection-panel.png"}})

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