v2.5.4 for Blender 3.5+

Minor bug fix creation of biological assembly nodes. Fixes #191

v2.5.3 for Blender 3.5.0+

Cryo-EM .map support

Along with several bug fixes and refactoring, the big news is that 2.5 brings support for import .map files for Cryo-EM maps 🥳

Because of this, MolecularNodes is only available with Blender 3.5 and above

This is thanks to Blender now shipping with pyopenvdb as part of the core library, and the addition of a new dependency mrcfile for reading the .map files themselves. Maps imported this way should align with corresponding PDB structures imported via other methods.

EM-specific Nodes

Only a couple of nodes have been created for dealing with EM density data so far. There is the choice of surface and wire as a representation by thresholding the density and generating mesh (which most users will be familiar with). As the density is imported as a volume, Blender sees it as smoke; thus, it can be shaded as an actual density.

Secondary Structure

With the updated biotite to 0.36.1, structures are now imported with a secondary structure attribute in the form of an integer, specifying if part of an alpha-helix, beta-sheet or looping / unstructured region. No nodes have been created to specifically take advantage of this data yet, but the field is available for users to get creative.

What's Changed

• Create qurto-publish.yml by @BradyAJohnston in #179
• Fix consistency in load_trajectory function call by @janash in #182
• Attribute secondary structure of proteins by @OLaprevote in #160
• Refactoring of package management and installation. by @YaoYinYing in #172
• Bring density up to date with main by @BradyAJohnston in #184
• intiial support for CryoEM .map import in Blender 3.5 by @BradyAJohnston in #164

New Contributors

• @janash made their first contribution in #182
• @OLaprevote made their first contribution in #160
• @alisterburt helped with code review in #164

Full Changelog: v2.4.3...v2.5.3

v2.4.3 for Blender 3.4.X

Bump version of biotite to install to be 0.36.1.

v2.4.2

What's Changed

• Fixes Blender crash when import via MDAnlysis with a import filter on topology that has bond information (#174) by @kimjoyc in #177

New Contributors

• @kimjoyc made their first contribution in #177

Full Changelog: v2.4.1...v2.4.2

v2.4.1 for Blender 3.4.1+

Minor fix for custom selections through MDAnlysis that were broken in version 2.4.1.

v2.4.0 for Blender 3.4.1

A new set of nodes to make it easier to create custom numeric selections, as well as improved package installation and logging on failure. Mostly thanks to @YaoYinYing !

What's Changed

• Customized Residue ID selection by @YaoYinYing in #149
• Refactor dependencies setup stuff by @YaoYinYing in #162

Full Changelog: v2.3.1...v2.4.0

v2.3.1 for Blender 3.4.1+

What's Changed

• Fix non-English error when New Data translation is disabled. by @YaoYinYing in #147
• add chain_id_unique on md import by @BradyAJohnston in #156

Full Changelog: v2.2.3...v2.3.1

v2.3.0 for Blender 3.4.1+

Big thanks to @YaoYinYing for fixing a long-standing bug of non-english languages breaking the addon. Additionally the Biological Assembly node works as expected again.

Added

• Panel for adding multiple selection strings, which will become boolean attributes on the imported model when importing via MDAnalysis.

Fixed

• Ball and stick node spheres now support field input for scaling the radius
• Error with initial node setup breaking when in non-english Blender UI (#139) contributed by @YaoYinYing
• Problems with biological assemblies failling on larger structures. (#143)
• Problem with Animate Frames node defaulting to wrong from range on start

v2.2.2 for Blender 3.4.X

Minor fix with usage of np.bool being deprecated in newer versions of Numpy and breaking import.

v2.2.1 for Blender 3.4.X

Added

• multi-model b_factor is added when importing from .pdb files via biotite #133
• 'Invert' field option to atom_properties and other selection nodes to optionally invert the selection
• Added better detection of ligands and modifcations (such as sugars) and a separate selection node for them. Currently ligands are stored on the res_name attribute, starting at 100 and incrementing one for each unique ligand. (should mostly address #79)

Fixed

• include_bonds option was not being utilised on MD import #132
• MOL_animate_res_wiggle was wiggling the OXT (res_name == 38) oxygen when a peptide chain ended. Added additional selection to not wiggle this atom, which should only ever appear when a peptide chain terminates.
• fixed import of vdw_radii for elements not supported by biotite (such as Fe) by moving vdw_radii to the data dictionary rather than relying on a function from biotite which had a limited dictionary for vdw_radii lookup