gelly Documentation

Contents

• Introduction to gelly
  • What is gelly?
  • This manual
  • Contact the authors
  • Using gelly within BUSTER
  • Doing geometry-only regularisation with gelly refine script
  • gelly command line options

• Similarity restraints in Gelly
  • Conventional approaches to NCS restraints
  • Local Structure Similarity Restraints (LSSR)
  • Target Restraints: Exploiting structural similarity to an already known structure

• Appendix A: Defining atom sets in gelly
  • The NOTE BUSTER_SET card
  • Using copy to create a set
  • The intersect operator: &
  • The union operator: +
  • The complement operator: \ absolute mode
  • The complement operator: \ relative mode
  • LISTing the atoms in a set to output log
  • Automatic/dictionary defined atom sets

• Appendix B: Parameter selection in gelly
  • Parameter selection overview
  • Holding parameters fixed with the NOTE BUSTER_CONSTANT card
  • Grouping parameters together with the NOTE BUSTER_COMBINE card
  • Defining groups for each residue with the NOTE BUSTER_COMBINE_RES card
  • Resetting previous parameter selection with the NOTE BUSTER_RESET_CONSTANT_COMBINE card

• Appendix C1: Similarity restraints: command line arguments
  • Overview
  • Automated setup of LSSR for NCS
    • automated NCS command line option -autoncs
    • autoncs and pruning, the -autoncs_noprune option
    • autoncs* setting the weight with -autoncs_weight value
  • Automated LSSR setup to an external target pdb structure with -target filename.pdb
    • Setting the weight for automated target restraints with -target_weight value
  • Swapping equivalent atoms to improve NCS and/or target restraints with the -sim_swap_equiv or -sim_swap_equiv_plus options
  • Manual adjustment of LSSR restraint conditions starting from the automated options
• Appendix C2: Similarity restraints: .Gelly card specifications
  • Overview
  • Defining similarity groups for NCS with the NOTE BUSTER_SIM_DEFINE card
    • Using LSSR restraints for a similarity group with the NOTE BUSTER_SIM_RESTRAIN_LSSR card
    • Using RMSD based positional restraints for a similarity group with the NOTE BUSTER_SIM_RESTRAIN_RMSD card
    • Using temperature factor restraints for a similarity group with the NOTE BUSTER_SIM_RESTRAIN_B card
    • Joining together different similarity groups with the NOTE BUSTER_SIM_JOINT card (useful for including water in NCS)
  • Support for old-style methods of defining NCS: CLUSTER and NOTE BUSTER_NCS_SOFT cards
  • Specifying target type restraints with gelly cards
    • Specifying target structure coordinate files with the NOTE BUSTER_TARGET01 card
    • Defining similarity groups for target restraints with the NOTE BUSTER_SIM_DEFINE card

• Appendix D: Utility restraint terms in gelly
  • Restraint on the distance between two given atoms: NOTE BUSTER_DISTANCE
    • Using utility distance restraints across a cell symmetry operation (for special positions)
  • Restraint on the angle between three given atoms: NOTE BUSTER_UTILANGLE
  • Restraint on the torsion angle between 4 given atoms: NOTE BUSTER_UTILTOR
  • Restraint on the sum of occupancies for multiple atoms: NOTE BUSTER_OCCSUM

• Appendix E: CHIRAL restraints in gelly
  • CHIRAL Restraints: Summary
  • The gelly CHIRAL Restraint term
  • Background work for the chiral restraint term

• Appendix F: Handling special position atoms and ions
• Appendix G: External libraries used