PROCHECK-NMR Operating Manual

7. Selecting model- and residue-ranges

By default, the AQUA and PROCHECK-NMR programs will analyze all the models in the ensemble and will include all their residues.

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.

Defining the selection file

The first step is to list the model- and residue-ranges you require in a simple ASCII text file (see example ). Make sure you define one range per line. The text can be entered in upper or lower case.

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).

MODEL and RESIDUE Keywords

The MODEL (or MODELS) keyword must be at the start of any line defining a range of model-numbers. On the other hand, the keyword RESIDUES is optional (the program assumes that if the string "MODEL" is not present then the line must be specifying a residue range).

Chain IDs

Where the protein structure contains different chain identifiers, these can be added after the residue number, and separated from it by one or more spaces. For example,

    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.

Restraints

Where you have used residue ranges to select only parts of the structure to be analysed there may be NOE, etc. restraints that span between residues and those that have been excluded. You can determine whether such restraints are to be included in the AQUA and PROCHECK-NMR analyses or not.

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

Other keywords

To make the definition of the ranges simpler, there are several special keywords you can use:

TO - is an optional keyword that can be used for separating the start and end of the range. For example
FIRST - refers to the first model in the ensemble or the first residue of a given chain. For example:
Here 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.
LAST - refers to the last model in the ensemble or the last residue of a given chain. For example:
Here 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.
ALL - can be used to specify all the models in the ensemble or all residues of a given chain. For example:
Here all models would be included and all residues of chain A.

Comments

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 example,

    % Best models:-
    MODEL 1
    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.