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autoBUSTER Documentation
Additional tools
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autoBUSTER Documentation : Additional tools
Copyright © 2003-2013 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
[email protected]
Contents
checkdeps - check that all 3rd party tools needed work properly.
corr - calculate real-space correlation ligand fragments into difference density
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 - use MolProbity 'reduce' to hydrogenate a protein with 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 header
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
Introduction
Running the tool
Anomalous difference Fourier map
Fo-Fo Difference map
ana_diffmap_residue - analyse difference map around specific residues
References
checkdeps check that all 3rd party tools needed work properly.
This is a utility that will check programs in the BUSTER suite in turn. checkdeps makes sure that all the required 3rd party
tools are installed, available and function properly. Problems are indicated on lines starting "ERROR". If no problems are
found then this is shown by "SUCCESS". The utility prints out a summary of results found at the end. The script's exit status
will be 0 for success but 1 if any problem is found
currently checkdeps runs:
refine -h to check licence is OK.
grade -checkdeps
grade_PDB_ligand -checkdeps
hydrogenate -checkdeps
buster-report -checkdeps
09 May 2014
BUSTER documentation
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