autoBUSTER Documentation

Copyright	© 2003-2015 by Global Phasing Limited
	All rights reserved.
	This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.
Contact	buster-develop@GlobalPhasing.com

Contents

1. Introduction
   • Scope and intended use
   • How to cite use of BUSTER
   • Authors and contributions

2. Installation
   • Prerequisites & remarks
   • Installing

3. File formats
   • PDB
   • MTZ
   • Rigid-body description
   • NCS description
   • TLS description
   • TNT sequence file and geometry libraries

4. Usage
   • Running the "refine" command
   • Command line arguments for the "refine" command
   • Controlling the number of threads used by BUSTER
   • Picture generation with Pymol
   • Automatic restraints generation

5. Examples
   • Normal refinement
     • Results available
     • Handling of waters
     • Rigid-body refinement
     • NCS restraints
     • B-factor refinement
     • TLS refinement

   • Some ligand is (possibly) present, but location is not well known
   • A ligand is (possibly) present, and the location is well known
   • A ligand is (possibly) present, and the location is well known: variation
   • Some settings that might need adjustment

6. Advanced features
   • The .autoBUSTER system of files and advanced command-line syntax

   • The macro feature

   • Grouped list of parameters, affecting ...
     • the generation of the TNT sequence file
     • the various checks performed
     • the refinement strategy
     • the analysis for potential, bound ligands
     • solvent structure (water) updating
     • handling of geometric restraints
     • handling of internal cavities (voids)
     • final analysis
     • creation of final PDB file

   • Some parameters most likely to be of interest
     • Program for water updating and Water updating criteria
     • Type of B-factor refinement
     • Geometric restraint weights
     • X-Ray weights
     • extra arguments to GELLY

7. Additional tools
   • checkdeps - check that all 3rd party tools needed work properly.
   • corr - calculate real-space correlation
   • gelly_refine - interface to GELLY (geometric refinement)
   • graph_autobuster_recipCC - view reciprocal-space CC plot
   • graph_autobuster_R - graph Rwork and Rfree during refinement
   • graph_autobuster_QM - graph QM energy during refinement
   • hydrogenate - add hydrogen atoms to protein and/or ligands
   • mk_coot_macros.sh - generate macros to use with Coot
   • mk_pymol_macros.sh - generate macros to use with Pymol
   • pdb2seq - generate TNT sequence from PDB
   • pdbchk - check (and optionally fix) PDB files
   • seq2seq - generate TNT sequence from ASCII file
   • pdb2dpi - calculate various versions of the "diffraction-component precision index"
   • pdb2occ - generate template for refining occupancy from PDB file
   • pdb2tls - extract TLS information from PDB file
   • refmacdict2tnt - convert REFMAC-format dictionary to TNT format preserving atom-type information
   • visualise-geometry-coot - launch coot to see BUSTER refinement result
   • diff_fourier - calculate (and analyse) various types of difference Fourier maps
   • ana_diffmap_residue - analyse difference map around specific residues
   • fetch_PDB - fetch coordinates and reflection data from local or online PDB archive (and convert reflection data to MTZ format)

8. Integration between autoBUSTER and coot
   • visualise-geometry-coot - launch coot to see BUSTER refinement results
   • BUSTER button - run BUSTER refinements from within coot

9. buster-report
   • Using buster-report
   • buster-report command-line options
   • External tools used by buster-report
   • Support for Mogul with additional in-house libraries
   • Support for ligand corporate or database IDs

10. References

11. Appendix 1 (alphabetical list of parameters)