Quick input guide: tutorial 4

Rigid-body Refinement of a Molecular Replacement model

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 Molecular Replacement solution. XYZ's for these atoms will be refined by BUSTER-TNT, each of the 6 monomers in the a.u. being treated as a rigid body
Chemical composition	1410 water molecules declared missing, one for each of the 6x235=1410 residues in the a.u.; the missing water molecules are given a B of 50, much higher than the average B of the atoms in the partial model (33).
Missing atoms prior envelope	No missing atoms are declared.
Solvent content	0.67: this estimate is based on the nominal 235x6=1410 residues in the asymmetric unit
Refinement: additional commands for the minimiser	COMBINE XYZ A|1 - A|235 COMBINE XYZ B|1 - B|235 COMBINE XYZ C|1 - C|235 COMBINE XYZ D|1 - D|235 COMBINE XYZ E|1 - E|235 COMBINE XYZ F|1 - F|235: each of the six monomers, chains A,B,C,D,E and F, from residue 1 to residue 235, will be treated as a single rigid body;
Bfactors Refinement: off	The individual B factors of the atoms are kept constant - TNT cannot perform simultaneous individual B refinement and rigid-body refinement.
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	Irrelevant as there is no contribution from stereochemistry. Set here to the default value of 3.5
Stereochemical restraints libraries	Only $BDG_tntdata/contact.dat is included, because the internal stereochemistry is not changed. The files $BDG_tntdata/csdx_protgeo.dat and $BDG_tntdata/bcorrel.dat would be needed when the proper structure refinement is started.