3DBIONOTES v3.10.0

Minor fix home page

Increased image quality on Homepage "Selected entries" carrousel

Fix loaders and manage errors

Main changes:

Separate the errors that are related to the viewer and those that are related to data.
Removed clipping
Fix MolecularStructure for undesired loads
Added toasts to pdbe-molstar
Decouple UniprotID (as 8UYS)

Fixes:

If main PDB is set hidden on URL params on init is not being applied on molstar (only on UI state)
If chain is added on URL params on init, highlight doesn't occur
Fix "Load PDB data" after any change on selection or visual change
When EMDB is set hidden, it shouldn't trigger new "Load PDB data"

Fix pdbe-molstar not loading correctly after exiting ligands view

Previously, after exiting the ligands view, every model (except the main PDB) wouldn't be added to Molstar canvas. Also, the ligand selector would be removed. This behavior was not happening because some strange useEffect was causing ligands to be empty [ ], but instead, because the method used when updating Molstar was only happening when the ligand was changed: it only was loading the main PDB and also with the default label; that's why when reading the structure tree, ligands wouldn't be found.

That behavior has been changed by forcing the plugin to update visually again and specifying the additional models. And also changing the method to specify the label of the main PDB.

Upgrade protvista-pdb

The main issue was happening when different blocks had different zooms on tracks. For that reason, when hovering over the Molstar sequence, sometimes the thin highlight wasn't being shown on tracks. Later when hovering on some track annotation, that thin highlight was only removed from that block and not the other ones (protvista-pdb instances).

Some key features/fixes:

Highlight Molstar selection even with zoom is out of range (added highlight on NavigationBar)
Highlight Molstar selection and track annotations on NavigationBar to occur in all blocks
Click on track annotation to make highlight stay, and highlight on NavigationBar in all blocks
Protvista menu action "Highlight fragments": to also show on NavigationBar on all blocks
Undo highlight action on tracks to be present on all blocks when some highlight occurs
Molstar highlight when clicking on some track annotation
Added highlights also on ProtvistaSequence
Main "highlight" action, to update to "Undo highlight" when highlight occurs
Main "Reset" action, removes all highlights (also on Molstar)
Highlight color on molstar is now the color of the track annotation
Main "highlight" action to behave as the "click" highlight
Main "highlight" action to focus and highlight on molstar (color would be the generic / default)

Minor fixes:

Make icons don't shrink when the right panel is smaller (separate "View / Highlight" menu actions)
Both actions were being done separately. When the checkbox was checked, only the highlight occurred. When the checkbox wasn't checked, it was only applying the zoom. Both actions have been separated.
Added highlight on NavigationBar for Carbohydrates (spheres and cubes) that are offsite the range of the sequence
Hide the "More options" tooltip when the button is clicked again
Highlight small annotations as on the "Validation - Quality" block, to have a minimum visible width
On "More options" menu tooltip: remove the tooltip after action is triggered
Track annotation tooltip seems cropped or hidden when is too close to the right side of the screen
ProtvistaSequence handles were behind highlights
Protvista D3 errors on negative and/or missing values

Dependencies:

• Protvista-pdb v2.0.1-est-2: https://www.npmjs.com/package/@3dbionotes/protvista-pdb/v/2.0.1-est-2 & https://github.com/EyeSeeTea/protvista-pdb/releases/tag/v2.0.1-est-2
• Pdbe-molstar v3.1.0-est-2: https://www.npmjs.com/package/@3dbionotes/pdbe-molstar/v/3.1.0-est-2 & https://github.com/EyeSeeTea/pdbe-molstar/releases/tag/3.1.0-est-2

Release 3.9.2

• Fix IDR data in COVID-19 Structural Hub

Release 3.9.1

Fixes for feedback dialog

Release 3.9.0

First production release