SPRUCE 1.1.0

Spring 2020

This version of SPRUCE has been built using OEToolkits 2020.0.

New Features

With this release we now support loop modeling in proteins structures. The database, which has been built for modeling loops that are 4-20 residues long by default, is available for download in a platform-independent format.

This release contains two new applications:

  • LoopDB_Builder uses existing structures to build a dictionary of known loops that can be used in loop modeling of unresolved gaps in protein structures.
  • du2pdb converts the entire content of an OEDesignUnit to a PDB file.

Major bug fixes

  • The GetStructure application has been enhanced to prevent partial downloads. Retries and timeouts have been improved.

Minor bug fixes

  • The prefix input behavior has been standardized across all SPRUCE applications.
  • The input option --restrict_to_refsite is now being respected for both SPRUCE and EnumSites.
  • The -site_residue input option to EnumSites now performs correctly.
  • The GetStructure application now checks that the input PDB code contains 4 characters.
  • SPRUCE now fails if an MTZ file is specified but is not present or is unreadable.
  • The documentation around the -site_residue option used for APO structures has been simplified.