Spruce TK 1.2.0

Fall 2020

New features

Major bug fixes

  • A bug that caused some modeled loops to be missing the backbone NH hydrogen where the modeled loops were attached has been fixed.

  • Fragment numbers for build loops have been fixed to be consistent with the anchor residues where the loops are inserted.

  • A bug in OEFixBackbone has been fixed to ensure that OXT atoms are always built on C-terminal residues.

  • An issue with atom order for built pieces like loops or caps has been fixed to ensure that these are sequential with the location they are built.

  • A bug in OEBuildLoops that in specific situations caused incorrect detection of gaps in protein structures has been fixed. Additionally, options have been exposed in OELoopBuilderOptions to allows users to control the underlying sequence alignment in the event of a failure.

Minor bug fixes

  • Improvements have been made to standard amino acid residue perception when preparing structures.

  • Site residues in OEMakeDesignUnits are now being checked against all the biological units so one can serve as a reference for the rest.

  • A bug in loop modeling that caused the function to create residues with identical residue numbers has been fixed. The function now properly builds using insertion codes.

  • A bug in loop modeling that caused problems for the underlying sequence alignment code and incorrect loops when a single residue was floating in space between two gaps has been fixed.

  • The chemical component dictionary used internally in OEMakeDesignUnits has been updated with the latest changes from the RCSB, including some fixes for incorrect entries in the source data based on rules and literature searches.