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
← →	Form	Step to the previous or next record, while the form has focus
Alt+↑ / Alt+↓	Form layout, a table’s field list	Move the focused field up or down
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.

These are imported on the Data tab. Each field’s type is worked out from every value in the file, and shown on the Dataset node.

A blank cell counts as a missing value, not as a different type, so a numeric column with gaps is still numeric. A column holding a word where a number is expected — NA, say — is read as text. Use Edit fields… on the Data tab to make that column a number.

Where things are stored

Everything you save is kept in the project’s database, beside its datasets:

A saved visualisation	Nodes, connections, views, layouts and per-chart settings, with the name you gave it, who first saved it and when, and who last saved it and when
Preferences	The Defaults and the named Presets from Settings
App settings	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. They are not files you can see in the project’s file list: to take a visualisation out of the application, or bring one in, use Export and Import.

Troubleshooting

“No dataset connected or data not loaded” — the chart has no Dataset node wired to its dataset input, the Dataset node has no dataset chosen, or the dataset is still loading. Check the Design tab for a missing connection, and the Data tab for the dataset.

A chart shows fewer rows than the dataset has — a filter on the dataset is hiding some (the Dataset node says Filtered: N of M rows, and so does the Data tab). Use Clear filter on the Data tab to see them all.

“Field … is not in the dataset — renamed or deleted?” — a chart is bound to a field by name, so renaming (or deleting) the field in Edit fields… leaves the chart pointing at a name that no longer exists. The chart keeps that name rather than quietly switching to another field: its node shows it as name (not found). Choose the field again, on the chart’s node or, where the message says so, in the chart’s ⚙ settings. Renaming the field back also restores the chart.

“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 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 that was imported as text. Check the type on the Dataset node; if it is wrong, fix the values in the file and import it again on the Data tab.

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.

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.

Saving says it needs the project database. This instance was started without one, so it can show charts but cannot keep a visualisation. Launch it again from the Data Manager, which provides the database.

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.