CE-Symm 2.2.2

Released 2 February 2022

Bug Fixes:

• Fix NullPointerException when loading files without PDB Ids (#113)
• Update to biojava 6.0.5

CE-Symm 2.2.1

Released 5 January 2022

Bug Fixes:

• Upgrade to BioJava 6.0.4

CE-Symm 2.2.0

Includes both CE-Symm and QuatSymm.

This version requires Java 8 or newer, and is tested up to Java 17.

Bug Fixes

• Fix Log4j vulnerabilities (CVE-2021-44228 and related). Includes log4j 2.17.1
• Fix errors when using RCSB services (e.g. fetching domains)
• Fix issue with Jmol not displaying correctly in european locales
• Fix issues with older Java versions due to various dependencies (#104)
• Upgrade to BioJava 6.0.3

Removed Features

• Remove ScanSymmetry class

CE-Symm 2.2.0 Alpha1

This is an alpha release. It is meant to fix critical errors introduced by the discontinuation of legacy RCSB services.

Bug Fixes:

• Fix errors when using RCSB services (e.g. fetching domains)
• Fix issue with Jmol not displaying correctly in european locales

Removed features:

• Remove ScanSymmetry class

The release was built using BioJava 6.0.0-SNAPSHOT c600773.

CE-Symm 2.1.0

Includes both CE-Symm and QuatSymm.

This version requires Java 8 or newer.

New features:

• Use BioJava 5.2.0, which brings lots of improvements:
  • Support Java 8-11 (#97)
  • Improved structure parsing (e.g. better symmetry operator support, mmCIF & MMTF parsing, better distinction between asymm_id and auth_id for identifying chains, etc)
  • Newer Jmol version
• Better documentation (#96)
• Separate QuatSymm package

CE-Symm 2.0.0

This is the final release for CE-Symm 2.0.

Documentation

CE-Symm 2.0 includes a plethora of major new features, including:

• Multiple alignment between all repeats of the protein
• Detection of multiple axes of symmetry (both dihedral point groups and hierarchical symmetry)
• Detection and visualization of point groups
• Better symmetry detection
• Monte-Carlo alignment optimization
• GUI/visualization improvements
• Major command line option changes
• Based on BioJava 4
  • Diverse input formats (pdb, mmcif, local & remote files, chain & residue selections)
  • Numerous bug fixes & improvements

Changes since cesymm-2.0-RC3:

• Update to BioJava 4.2.12
  • Fixes several upstream bugs (#91 #92 biojava/biojava#703)
  • Update external resources (SCOP, PDB)
• Increase heap size in runCESymm.sh (#94)

CE-Symm 2.0 Release Candidate 3

Fixes an upstream bug in RC2 by updating to BioJava 4.2.8

CE-Symm 2.0 Release Candidate 2

This is a second beta release for CE-Symm 2.0.

Documentation

Changes since RC1:

• Add --axes output
• Improved alignment optimization for hierarchical symmetry
• Better visualization of hierarchical symmetry
• Bug fixes for biological assemblies & other glitches

CE-Symm 2.0 Release Candidate 1

This is a beta release for CE-Symm 2.0.

Documentation

CE-Symm 2.0 includes a plethora of major new features, including:

• Multiple alignment between all repeats of the protein
• Detection of multiple axes of symmetry (both dihedral point groups and hierarchical symmetry)
• Detection and visualization of point groups
• Better symmetry detection
• Monte-Carlo alignment optimization
• GUI/visualization improvements
• Major command line option changes
• Based on BioJava 4
  • Diverse input formats (pdb, mmcif, local & remote files, chain & residue selections)
  • Numerous bug fixes & improvements

CE-Symm 1.0.0

This is the initial release of the CE-Symm tool. It corresponds to the version used in the publication

Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic Detection of Internal Symmetry in Proteins Using CE-Symm. Journal of Molecular Biology, 426(11), 2255–2268. doi:10.1016/j.jmb.2014.03.010