Reference
Keyboard
| Key | Where | What it does |
|---|---|---|
Delete / Backspace |
Design tab | Delete the selected node or connection |
Enter |
Renaming a tab or node | Confirm |
Escape |
Renaming | Cancel |
Escape |
Interaction map | Clear the ligand selection and any column filter |
Escape |
Interaction diagram | Release a pinned highlight |
← → |
Interaction diagram | Step to the previous or next ligand, while the panel has focus |
Home / End |
Interaction diagram | Jump to either end of the set |
| Scroll | Design tab | Zoom the canvas |
File formats
| Kind | Extensions | Notes |
|---|---|---|
| Structures with data | .sdf, .sd |
Each record’s structure becomes the molecule field; SD tags become columns |
| Tabular data | .csv, .tsv, .tab |
The delimiter is detected; quoted fields are handled |
| SMILES lists | .smi, .txt |
|
| Protein structures | .pdb, .mmcif, .cif |
For FileSelector nodes, not as datasets |
Compressed forms — .sdf.gz, .csv.gz and so on — are read directly.
Each field’s type is inferred by sampling the file, and shown on the Dataset node. Where it is wrong — an identifier made of digits that should be a label, say — Edit schema… on that node corrects it.
Where things are stored
Everything is inside the project, in a .visualisations directory:
<name>.viz.json |
One saved visualisation: nodes, connections, views, layouts and per-chart settings |
preferences.json |
The Defaults and the named Presets from Settings |
app-settings.json |
Whether Auto save is on |
Because they are in the project, they are shared with everyone who has access to it and outlive any one instance of the application.
Troubleshooting
“No dataset connected or data not loaded” — the chart has no Dataset node
wired to its dataset input, or the dataset is still being scanned. Check the
Design tab for a missing connection.
“Configure X and Y fields on the wiring canvas” — the chart’s required fields are not set. They are the dropdowns on the node itself, not in the ⚙.
“Apply a filter to display molecules” — the molecule grid or 3D viewer has
Require filter on, which is the default. Wire a selection into its filter
port, or turn the setting off if the dataset is small enough to draw whole.
“Apply a filter to compute interactions” — the same guard on an interaction view. Detection costs about 40 ms per ligand, so it waits to be told which ligands matter.
“Connect a FileSelector with a receptor structure” — an interaction view has
no protein to compute against. Add a FileSelector holding a PDB or mmCIF file
and wire it to the view’s files port.
The interaction map is empty, or a residue’s NH and CO boxes never fill. Usually the data rather than a fault. Backbone contacts are much rarer than sidechain ones, and a receptor with no waters or metals can never show water-mediated or metal-coordination interactions. If it is empty entirely, check that the poses and the receptor share a coordinate frame: poses docked into a different copy of the protein produce no contacts at all.
A chart shows nothing and the status bar says everything is missing. The field is not the one you think it is — a text column chosen as an axis, or a numeric column the scan read as text. Check the type on the Dataset node, and correct it with Edit schema… if need be.
A chart shows nothing and the status bar says everything is out of range.
An axis minimum or maximum you set is excluding the data. Clear the box to
return it to auto. A log scale does the same to zero and negative values.
“3D rendering is unavailable: WebGL could not be initialised” — the browser cannot use the graphics hardware. Enable hardware acceleration in the browser’s settings and reload.
A file you know is in the project is not offered. Only the extensions above
are listed, and anything inside .visualisations is deliberately skipped.
A FileSelector says a linked file is not available. The visualisation was saved against a project that had that file. Pick the file again from Add available file….
A preset name reads “not defined”. The visualisation names a preset that this project’s settings do not have. The chart falls back to Default values. Recreate the preset under Settings → Presets, or point the chart at one that exists. See Presets belong to the project.
A popped-out window is frozen. A window that is completely covered, or on a closed laptop lid, stops being drawn by the browser. Reveal it and it resumes.
The application stopped responding after a while. An instance left idle is shut down by the Data Manager. Your saved visualisations are in the project; launch a new instance and load them.
Known limitations
- A structure drawn in a MoleculeSketcher is not saved with the visualisation. Loading one gives you the wiring and the settings, but an empty sketcher — anything downstream of it will ask for a structure again.