BUSTER User Manual
Barnase Soft-NCS tutorial

Quick input guide: tutorial 2

BUSTER NCS-restrained refinement of a 25% 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

21x3=63 missing residues
One additional oxygen atom for each of the 3x110 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 (<B>=14).

Missing atoms prior envelope Uniform: this is the simplest choice, amounting to distributing the missing atoms anywhere but where the partial structure atoms are. If you wanted to improve on this, you could select: "From current phases": the current 2Fo-Fc map would be used to define the regions where the missing atoms are expected to be

Solvent content 0.43%, as estimated from the nominal 3x110=330 residues in the a.u. of the P32 unit cell

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.

TNT soft-NCS file Just one line, to restrain shifts for three chains to be similar: CLUSTER PROT CHAINS A B C

TNT soft-NCS weight Set to 50, roughly corresponding to an 0.14 Å rmsd between atomic xyz's of the three copies

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

Input item	Notes
Partial Structure	The PDB file with the atoms whose xyzB's will be refined by BUSTER-TNT
Chemical composition	21x3=63 missing residues One additional oxygen atom for each of the 3x110 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 (<B>=14).
Missing atoms prior envelope	Uniform: this is the simplest choice, amounting to distributing the missing atoms anywhere but where the partial structure atoms are. If you wanted to improve on this, you could select: "From current phases": the current 2Fo-Fc map would be used to define the regions where the missing atoms are expected to be
Solvent content	0.43%, as estimated from the nominal 3x110=330 residues in the a.u. of the P32 unit cell
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 `$BDG_home/bin/buster/pirToSeq.pl` starting from an ASCII 1-letter sequence file for the full protein
Weight on the x-rays residual	Set to 3.5 - a value low enough to keep a fairly tight stereochemistry.
TNT soft-NCS file	Just one line, to restrain shifts for three chains to be similar: `CLUSTER PROT CHAINS A B C`
TNT soft-NCS weight	Set to 50, roughly corresponding to an 0.14 Å rmsd between atomic xyz's of the three copies
Stereochemical restraints libraries	`$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

Eric Blanc, <blanc@GlobalPhasing.com>

Pietro Roversi, <pietro@GlobalPhasing.com>

Last modified: Fri Jan 9 11:24:09 GMT 2004