BUSTER User Manual
IF3-C tutorial

Quick input guide: tutorial 1

BUSTER refinement of 30% incomplete structure

This tutorial has been run in the "Standard" user level. In this mode, default values are used for most of the input items. The ones that needed some extra attention are described below:

Input item	Notes
Partial Structure	The PDB file with the atoms whose xyzB's will be refined by BUSTER-TNT
Chemical composition	63 missing residues One additional oxygen atom for each of the 95 residues of the full protein (to mimic ordered water molecules) The missing atoms are given a slightly higher B value than the average B of the atoms in the partial model.
Missing atoms prior envelope	Based on the current phases: the program will run a scaling-only calculation first, followed by a refinement that uses the 2Fo-Fc map from the first run to define the envelope for the missing atoms.
Solvent content	from solvent content optimisation in SHARP.
Refinement: additional commands for the minimiser	RANGE B 1 300: no B factors will refine below 1; atoms whose B factor wants to refine above 300 will be rejected
TNT sequence file	Was prepared with the script $BDG_home/bin/buster/pirToSeq.pl starting from an ASCII 1-letter sequence file for the full protein
Weight on the x-rays residual	Set to 3.5 - a value low enough to keep a fairly tight stereochemistry.
Stereochemical restraints libraries	$BDG_tntdata/csdx_protgeo.dat: geometry of standard amino-acids $BDG_tntdata/bcorrel.dat: temperature factors correlation restraints for standard amino-acids $BDG_tntdata/contact.dat: basic non-bonded distances for most commonly occurring atom types