However, it is sometimes useful to analyze only some of the models and/or obtain statistics for only selected regions of those structures (for example, only the well-defined core regions of the protein, or those corresponding to clearly-defined regions of secondary structure).
This section describes how you can define both which models and which blocks of residues you want included in the AQUA analyses and the PROCHECK-NMR plots.
A simple example, might be:-
MODELS 1 TO 4 MODEL 8 MODELS 10 TO 15 RESIDUES 6 15 RESIDUES 20 32 RESIDUES 40 48
Here, only models 1, 2, 3, 4, 8, 10, 11, 12, 13, 14 and 15 would be selected. In each one, the analyses would include only residues in the ranges 6-15, 20-32 and 40-48.
If you want to include all the models, then remove all model ranges from the file (or use "MODELS ALL", as described below). Similarly, to include all the residues, just remove all residue ranges. (Note that: for the viol2pdb program, the absence of any model ranges in this file implies that only Model 1 is to be used, rather than all models).
RESIDUES 6 A 15 A RESIDUES 6 15 A RESIDUES 45 A 12 B
Wherever both residues defining the range are in the same chain (as in the second line above), then the chain need only be entered once (as above). Thus, the first two lines above are equivalent.
By default, all restraints involving the selected residues will be included. If you want to include only those which are between the selected residues, then add the command "BOTH" anywhere in the selection file. For clarity, you can incorporate the word into some meaningful text, as follows:
RESTRAINTS ONLY WHERE BOTH RESIDUES ARE SELECTED
MODELS 1 TO 4 RESIDUES 5 A TO 15 A
MODELS FIRST TO 4 FIRST A TO 15 AHere the model range would be from the first model in the ensemble to model 4, while the residue range would be from the first residue in chain A to residue 15 in chain A.
MODELS 10 TO LAST FIRST A TO LAST BHere the model range would be from model 10 to the last model in the ensemble, while the residue range would be from the first residue in chain A to the last residue in chain B.
Here all models would be included and all residues of chain
Comment lines can be included in the file provided that the first character
of the line is either a % or a #. This allows you to comment
out previously defined ranges without having to delete them completely. For
% Best models:-
MODELS 3 TO 6
% Residue ranges:-
%RESIDUES 6 A TO 15 A
%RESIDUES 6 TO 15 A
RESIDUES 45 A TO 12 B
Here the first two lines defining the residue ranges have been commented
out and will be ignored by the program.
PROCHECK-NMR Operating Manual