v2.7.3 for Blender 3.5+

Minor fixes for cartoon style, and some refactoring of the docs.

What's Changed

• add selection to style cartoon by @BradyAJohnston in #241
• minor cleanup in docs by @BradyAJohnston in #242

Full Changelog: v2.7.2...v2.7.3

v2.7.2 for Blender 3.5+

Bump version for MDAnalysis in some more files to fix install.

v2.7.1 for Blender 3.5+

Mostly a fix to correct some weird bugs with the secondary structure cartoons on larger structures.

What's Changed

• Add release to Makefile by @BradyAJohnston in #234
• Fix oxygen selection bug in SS by @BradyAJohnston in #238
• Dev bump by @BradyAJohnston in #239

Full Changelog: v2.7.0...v2.7.1

v2.7.0

A lot of under-the-hood bug fixes and refactoring, but also the addition of using ESMFold to predict the structure of an AA sequence.

What's Changed

• Added ESMFold as structure import option by @wjm41 in #205
• Changes how docs are built to include python API by @BradyAJohnston in #222
• initial switch changing docs build by @BradyAJohnston in #223
• Molecular Nodes Documentation by @FL-ECHE in #219
• Dev: Add Initial testing suite by @BradyAJohnston in #225
• Dev: Refactor Initialisation and Organisation by @BradyAJohnston in #226
• Add new attributes such as lipophobicity by @BradyAJohnston in #131
• Dev: Fix small-molecule import by @BradyAJohnston in #227
• Dev: Fix codecov coverage.xml by @BradyAJohnston in #228
• Dev: Re-enable node-add menu by @BradyAJohnston in #229
• Dev: Fix cartoon helices and other issues by @BradyAJohnston in #230

New Contributors

• @wjm41 made their first contribution in #205
• @FL-ECHE made their first contribution in #219

Full Changelog: v2.6.2...v2.7.0

v2.6.2 for Blender 3.5+

Fixes some issues with initial boolean attributes to do with backbone selection. Additionally fixes some errors with surface generation and node duplication.

What's Changed

• tweak att_is_backbone() to include O by @BradyAJohnston in #208
• Improve atom_name and is_backbone by @BradyAJohnston in #209
• Stop node tree duplications by @BradyAJohnston in #210
• Fix surface split by @BradyAJohnston in #211

Full Changelog: v2.6.1...v2.6.2

v2.6.1 for Blender 3.5+

What's Changed

• Small fix to improve compatibility with starfiles & some bugs in SS annotation. by @tubiana in #203

New Contributors

• @tubiana made their first contribution in #203

Full Changelog: v2.6.0...v2.6.1

v2.6.0 for Blender 3.5+

New Features

.star File Import

@jojoelfe finished off the import of .star files from cisTEM and RELION, which enables instancing of structures onto datasets from EM tomography.

output.mp4

Secondary Structure Cartoons

Utilising the secondary structure information that is now imported or can be computed, cartoon styles can be created for alpha-helices and beta-sheets. Every aspect of the cartoon is controllable through fields, enabling animation and customisation by the user.

cartoon.mp4

What's Changed

• Update Readme and Installation Instructions by @BradyAJohnston in #194
• Support cisTEM starfiles by @jojoelfe in #196
• Add Support for Importing .star File by @BradyAJohnston in #161
• Take secondary structure from .mmtf file instead of calculating by @BradyAJohnston in #199

New Contributors

• @jojoelfe made their first contribution in #196

Full Changelog: v2.5.4...v2.6.0

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.