Bandicoot v0.2.1.0

BANDICOOT v0.2.1.0 - Ligand tools

• Ligand menu item re-activated with all the tools functional
• Ligand 2D now active (prints ligand 2D structure in bottom-left corner)
• FLEV now works (activate via Ligand -> FLEV this residue)
• Bandicoot recompiled in C++20 with RDKit bundled (makes all the above features work)

Bandicoot v0.2.1.1

BANDICOOT v0.2.1.1 - alt. conf. bond width scaling by occupancy

• alternate conformations rendered at different widths depending on occupancy (it's a coarse gradient with occupancy split into five brackets)
• only works with "Colour by Alt. Conf." display setting
• can be toggled in Edit -> Preferences -> Bonds -> Bond Parameters
• auto-scales to different default bond widths, though is less useful with bond widths less than 5 points

v0.2.0.1

BANDICOOT v0.2.0.1 - pre-release

Bugfixes:

• Generate Ligand Restraints picker now goes away after restraints are built
• pdb_string() no longer leaks entire PDB texts per call
• fixed dead print/refcount paths
• Python shutdown now runs on exit

Other changes:

• logs go to $PWD/bandicoot-sessions rather than to /Users//bandicoot-sessions
• README.md update
• SESSION_RECORDING.md introduced

v0.2.0.0

BANDICOOT v0.2.0.0

Bandicoot has been extensively rewritten to replace mmdb-based mmCIF I/O with gemmi. As a result, Bandicoot v0.2 now faithfully reads and writes coordinates in mmCIF format, preserving structural metadata with high fidelity.

Main features:

1. all mmCIF I/O is done with gemmi (model and dictionary stuff is still mmdb)
2. faithful read-in/write-out of mmCIF header information
3. auto-renaming of ligands with placeholder names (that have no known database entry)
4. auto-generation of ligand restraints (with selection and overwrite options)
5. Modelling -> Generate Ligand Restraints added, launches the same chooser dialog as auto-generation of restraints
6. preferences for ligand handling (Preferences -> Others -> Ligands) (previous tab named "Ligands" has been renamed to "panDDA")

Tweaks:

1. Fixed symmetry-copy ADP transfer
2. Save Coordinates and Save Symmetry Coordinates now use the same file dialog
3. Save dialog now allows explicit choice of file format
4. Ctrl-C in terminal now hard exits Bandicoot

Known Issues

• Automatic ligand restraint generation might fail and generate crappy restraints
• Some automatic ligand restraint generation might take a while (up to a minute) though that appears to be rare
• Ligand restraint generation dialog doesn't go away on "Generate Restraints" click if the dialog launched from Modeling -> Generate Ligand Restraints
• Drag/drop load doesn't work with maps (seems like it's true for all maps, though not all formats have been tested)
• Side toolbar style not preserved between sessions if changed via the Settings button (Preferences changes work fine)
• 5-character CCD codes truncate if saving in PDB format (this will never change, PDB format has been deprecated since 2012)

Bandicoot v0.1.4.15

BANDICOOT v0.1.4.15

Functionally the same as v0.1.4.14; all the changes are in the build scripts and documentation. Released to match the latest "build from source" version.

Bandicoot v0.1.4.14

BANDICOOT v0.1.4.14

New features (addressing corresponding issues):

Issue #21: Open Map button added to toolbar
Issue #22: Bonds (Colour by Alt. Conf.) display mode made default (Preferences -> Colours -> Bond Colours now allows users to establish their default display preference)
Issue #23: Option-Click now centers on atom (works with a trackpad); Option-Drag now pans the view, same as Ctrl-Drag

Bandicoot v0.1.4.13

BANDICOOT v0.1.4.13

Fixed issues:

• Duplicate GTK stack loaded at runtime
• Reference structures installed one directory too deep (reference-structures/reference-structures/), so nothing found them
• Stray build-machine rpaths in libjpeg and Pillow's bundled libjpeg

Bandicoot v0.1.4.12

BANDICOOT v0.1.4.12

New Feature:

• Alt. conf color coding! In Display Manager, select Bonds (Colour by Alt. Conf.) for the loaded molecule; residues with alternate conformations will be rendered in distinct colors; conf A will be shifted 20° (default) from the rest of the model, while conf B will be shifted 20° (default) from conf A. The shift magnitudes are individually configurable through Edit -> Preferences -> Bonds -> Bond Colours.

Fixed Issues:

• #15 - removed popup, deferred the rest to UI rebuild (upcoming)
• #16 - fixed sequence view closing bug, re-calibrated seq viewer by number of sequences, made that configurable in Edit -> Preferences -> General -> Dialogs
• #14 - made contour string position readjust based on whether there are top toolbars docked

Bandicoot v0.1.4.11

BANDICOOT v0.1.4.11

Issues fixed in this release:

• #7 — hydrogens drawn as phantom grey stars in Colour-by-Chain, duplicating with the real H sticks.
• #8 — bundled Python missing libexpat, so all XML parsing died on any Mac with system expat < 2.7.2.
• #9 — phenix.refine mmCIF files failed to load whenever the model had NCS operators.
• #10 — sidebar settings menu always showed "All Icons" regardless of the sidebar's actual state; sidebar settings menu collapsed to scroll arrows when opened near the bottom of the screen.
• #12 — phi/psi edit corrupted the model, displacing the two CA atoms 7–9 Å on accept.
• #13 — phi/psi edit left a stale fragment behind, silently blocking every subsequent edit.

Bandicoot v0.1.4.10

BANDICOOT v0.1.4.10 - Stand-alone version

This Bandicoot version has been extensively purged of a lot of dead files and folders and made fully stand-alone. Specifically:

• removed all dependencies on Homebrew and Conda, bundled all the necessary libraries and altered code where necessary; Bandicoot can now be installed on a system that doesn't have either Homebrew or any Conda variety
• removed ~280MB of static libraries from the build
• removed a vestigial call that launched XQuartz but didn't do anything else

As a result, Bandicoot is now an end-user app only; to use it as an API, developers will have to build their own version from source. Alternatively, a toolkit binary can be provided upon request.