     Ac_predciton and shift_plot: programs for analyzing 
          atomic shifts in unrestrained refinement
          
Unrestrained refinement is stable for the vast majority of 
atoms when working at atomic resolution. Nevertheless 
geometrical restraints should be held in refinement for 
residues that are present in several (alternative) 
conformations in the crystal used for the X-ray experiment; 
in the other case such residues deteriorate significantly. 
We believe that on the contrary, large distortion of a 
residue in unrestrained refinement may hint the presence 
of alternative conformations for this residue. To get these 
hints in a routine way we suggest two methods to analyze 
shifts of atomic centers resulted from several cycles of 
unrestrained refinement. The first method is a simple 
diagram plotting the values of atomic shifts against the 
residue number. It may give an idea of the crystallographic 
order of different parts of the structure at qualitative level. 

The second method is decision-making procedure which compose 
a list of residues that are likely to be present in 
alternative conformations or disordered and so should be 
checked thoroughly with Fourier syntheses, and included 
into the model with alternative conformations, when necessary. 
The parameters of the suggested procedures were estimated 
with the use of 203 PDB structures refined at resolution 
better than 1.2A. 

Both programs are designed to analyze atomic shifts during
unrestrained refinement. Therefore the user should perform
such a refinement and provide 2 .pdb files: the model before
refinement and the model after refinement.
To analyze a particular model, we offer to apply the Trial 
Unrestrained Refinement (TUR) consist of 
   Three macro-cycles of unrestrained refinement with 
   phenix.refine program.
or
   10 cycles of unrestrained refinement with Refmac

Shift_plot will produce a diagram of atomic shifts vs. residue 
number. The largest shifts indicate the residues that are 
considered in this approach as the main candidates to be 
present in alternative conformations, and should be checked first.
Shift_plot also may be used to analyze atomic shifts
resulted from any other model manipulation or refinement.
It matches atoms with the same:
-atom serial number;
-atom name;
-residue name;
-chain ID;
-residue number;
-insertion code.

AC_prediction implements automatic decision-making 
procedure that classifies every residue as single conformation 
or alternative conformations (SC and AC below). The procedure 
is based on the observation that SC-residues and AC-residues 
have different mobility in unrestrained refinement. The 
decision is made either by comparing the observed atomic 
shifts with a predetermined threshold, or comparing the 
probabilities of such shifts for SC and AC-residues. 


References:
1. O. V. Sobolev and V. Y. Lunin "Detection of alternative 
conformations by unrestrained refinement". Acta Cryst. D68.1118-1127.
2. O.V. Sobolev. DETAC: tools to detect alternative conformations 
by unrestrained refinement. (2012). 
Computational Crystallography Newsletter. 3.