Refinement and Modeling of a Point Mutant


In this example we have mutated one point residue Tyrosine 27 to a Tryptophan.  
We will start this exercise with the following files:

Exercise2.pdb		The native structure, used as a starting model
Exercise2.cell		The experimental cell constants and symmetry elements
Exercise2.fob 		The experimental diffraction intensities


We will be using the refinement program XPLOR to refine the atomic positions
of all the atoms in the model and the temperature (vibrational/disorder) 
factors associated with them.  The parameter files needed to perform these 
refinements are ready to be used by XPLOR.  The order in which these refinements 
should be performed is given in the following files:

Ex2_instructions.txt
Ex2_prep.com
Ex2_initial_refine.com
# Edit model in XtalView: Use brefinement.pdb and xplor.phs
				 Replace TYR 27 with TRP 
Ex2_refine.com
{ Check refined model in XtalView }  :Repeat this refinement until convergence
Ex2_refine.com


Please note the required names of all the input, and standard output file names.
Always save your model as you proceed, so that in the event of an error you
can recover your previous work.

Record the 'R' factor after each step of the refinement.  Note how the "R" 
factor decreases as the model is refined against the experimental data, and
increases as the resolution is increased.

use "grep "R=" *.log to keep track of the R factor.