Specifying Zones

The ZONE command is used to specify zones in the two structures which are considered equivalent. The complete syntax for the command is:

   ZONE CLEAR|((*|(X...[,n][/m])|(j-k))[:(*|(X...[,n][/m])|(j-k))])

where X... is an amino acid sequence, n is a number of residues, m is the occurrence number, j and k are residue specifications of the form [chain]resnum[insert]. Items in square brackets are optional and alternatives are marked by a | and grouped in parentheses.

ZONE commands are cummulative. Thus each zone you specify is added to those currently active. To clear all zones (i.e. fit all residues), the ZONE CLEAR or ZONE * command may be given.

Although it appears complex, the syntax is actually very simple and consists of two identical sections separated by a colon (:). The left half is applied to the reference structure and the right half to the mobile structure. In its simplest form, the right hand half of the expression is absent and the specification is applied to both reference and mobile structures. For example:

   ZONE 24-34

will set the zone to include residues 24-34 in both structures. If you wanted to fit 24-34 in the reference structure with 25-35 in the mobile structure, this simply becomes:

   ZONE 24-34:25-35

You may also specify chain names and insertion code. The chain name is placed before the residue number and the insertion code afterwards. For example:

   ZONE L25A-L30

fits residues 25A-30 in the L chain of both structures.

Simple wildcards may also be used. For example

   ZONE H*:B*

fits the reference H chain with the mobile B chain,

   ZONE -10:50-59

fits from the first residue to residue 10 in the reference structure with 50-59 in the mobile structure.

   ZONE *:1-100

fits all residues in the reference structure with 1-100 in the mobile structure.

If the structure file contains negatively numbered residues and you are using residue numbering, you can escape the minus sign in the residue number using a backslash:

    ZONE \-4-10:\-1-13

will fit residues -4 to 10 in one structure with -1 to 13 in the other.

Alternatively, you may specify the zones to be fitted by giving a sequence fragment. Together with that fragment, you may specify the number of residues to consider starting at that point. If the fragment occurs more than once in the sequence you may specify which occurence you wish to consider. For example:

   ZONE CAR:VNS

fits the first occurence of CAR in the reference set with first occurence of VNS in the mobile set;

   ZONE CAR,10:VNS,10

fits 10 residues starting at the first occurence of CAR in the reference set with 10 residues from the first occurence of VNS in the mobile set;

   ZONE CAR,5/2

fits 5 residues from second occurence of CAR in both structures;

   ZONE 24-34:EIR,ll

fits 24-34 in the reference set with 11 residues starting at the first occurence of EIR in the mobile set.

By default, ProFit works in `Residue Number' mode, i.e. the numbers used in zone commands are the numbers seen in the PDB file. The alternative mode is `Sequential' mode where residues are numbered sequentially throughout the structure (including throughout multiple chains). Any chain names appearing in zone specifications will be ignored in Sequential mode. To switch mode, you use the NUMBER SEQUENTIAL or NUMBER RESIDUE commands.