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DrAliEbrahim merged 2 commits into from
Aug 10, 2026
Merged

Update to user_guide.md #32

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Update to user_guide.md
Jun 30, 2026
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Jun 30, 2026
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16 changes: 13 additions & 3 deletions docs/source/user_guide.md
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Expand Up @@ -92,9 +92,9 @@ Geometric filtering allows you to limit hits based on their position in 3D space

<img src="_static/media/FilteringSphere.png" alt="lhs" width="600px">

This feature is **ON** by default and can be toggled in the Advanced Search dialog. If you turn it off, any existing geometric filtering is cleared and no spatial filtering will be applied.
This feature is **ON** by default. Open the "Advanced Search" menu using the filter icon, and toggle "Coordinate search" in the Advanced Search dialog. If you turn it off, any existing geometric filtering is cleared and no spatial filtering will be applied.

<img src="_static/media/AdvancedSearchDialog.png" alt="lhs" width="600px">
<img src="_static/media/AdvancedSearchDialog_2.png" alt="lhs" width="600px">

---

Expand Down Expand Up @@ -182,10 +182,20 @@ See also [Creating direct URLs to specific views](#creating-urls)

Snapshots are saved views of the current analysis state, allowing you to quickly return to a specific set of selected hits and visualisation settings, and making it easy to share or revisit a particular analysis.

To create a snapshot, click "Click to create new snapshot" at the bottom of the Snapshots window, or the "SHARE" button at the top of the Fragalysis interface. Both methods will create a new snapshot in the "Snapshots" interface.

```{image} _static/media/snapshot.png
:width: 600px
:alt: snapshot window
```
Each new snapshot will give you three interactive options:

| Control | Description |
|--------|-------------|
| **RENAME** | Allows the user to edit the name of the snapshot from the default date and time format. |
| **SHARE** | Copies the snapshot URL to the clipboard. |
| **UPDATE** | Updates the snapshot to the current orientation in the viewer. Note: this **does not** update the date and time in the snapshot. |

(creating-urls)=
### Creating direct URLs to specific views

Expand Down Expand Up @@ -422,7 +432,7 @@ Some examples of extra files:
| `affinity_files` | Subdirectory containing affinity data for specific datasets |
| `soakdb_[session_number].sqlite` | SoakDB file in SQLite format <br> - Experimental details for each crystal, including soaking conditions, data collection parameters, and processing results. |
| `soakdb_[session_number].csv` | SoakDB file in CSV format <br> - Experimental details for each crystal, including soaking conditions, data collection parameters, and processing results. |
| `protein-sequence.fasta` | Target sequence in FASTA format |
| `protein-sequence.fasta` | Target sequence* in FASTA format (*can be multiple sequences when multiple constructs are used) |

---

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