No, it’s not quite the end of August, but I start teaching on Monday, so it’s easier for me to draft this update now before life gets busier.
The extremely talented @aerkiaga finished up Google Summer of Code with some blockbuster new features.
It’s not just proteins - it makes everything clearer with real-time shadows:
In a series of patches, there’s now support for easily building a range of inorganic / organometallic complexes, or building out ligands and functional groups from hydrogen sites.
This now uses PubChem’s search capability (and thus over 100M compounds), including HTML formatting of superscripts / subscripts (and hopefully Greek letters)
I almost forgot … along the way, I merged support to determine bond orders from XYZ, Fchk, quantum formats, etc.
Please report bugs - I just fixed a bunch of them.
You can now generate the centroid or center of mass of the molecule or a selection of atoms, including a site perpendicular to the best-fit plane of the molecule (e.g., used to generate Cp ligands).
There are now “Copy As” SMILES and InChI commands (back from v1.x).
Selecting atoms is now undo / redo enabled.
Fixed a bug which wouldn’t properly add hydrogens when editing (#1112)
These files support multiple coordinate sets / disorder through “Alternate Location” sections. These are now properly supported and you can switch between them.
If you mis-typed a PDB code or otherwise had an invalid MMTF file, Avogadro could crash. That’s now fixed.
Previously, the bond-centric tool or editing in the properties table would not adjust torsions between rings. That’s now fixed.
Scroll wheel bug on Linux (#1065)
The scroll wheel was a bit flaky on Linux - it should be smoother now.