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Set the refinement map in the Cryo-EM tutorial
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pemsley committed May 21, 2024
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19 changes: 13 additions & 6 deletions blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md
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Expand Up @@ -20,8 +20,8 @@ At the moment, you will need to gunzip the map.
- (you can also use '[' and ']' to increase and decrease the map radius)

- **Map Tools** → **Sharpen/Blur map**
- B-factor to apply should be zero
- Turn on **use resample** and use the resample factor 1.4 → **OK**
- "B-factor to apply" should be `0`
- Turn on **use resample** and use the resample factor `1.4` → **OK**
- **Maps** → Click on the "Gear" icon on the (newly-created) Masked map → Draw settings → Activate "**Lit lines**"

You will see that this new map is more easy to interpret.
Expand Down Expand Up @@ -108,12 +108,19 @@ Moorhen generates extra restraints (shown in grey lines)
- **Maps** → "Gear" icon of the masked map → **set map weight**
- `1830` (it should be the default) → **Set**

To refine this domain/chain:
To refine this domain/chain, we need to tell Moorhen which map to use
for the refinement

- **Maps** → Click on the "○ Active" button of the masked map

The background of the button will turn black when it's active.

Now define which atoms we want to refine (in this case, all of the nanobody)

- **Edit** → **Create a selection**
- Molecule is `6gdg fragment`
- Atom Selection is `//` (i.e. "all atoms")
- **OK**
- Molecule is `6gdg fragment`
- 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 at the middle top
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