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Setup of Distance Restraints

Distance restraints consist of one of more ASSIgn statements. It is convenient to include these statements in a file. There are two selection statements that specify the atom pair(s) between which the distance information is included. The first statement selects the first atom (or set of atoms in the case of ambiguous assignments); it has to specify the actual residue number and atom name, e.g.,

resid 34 and name HN

which selects proton HN attached to N of residue 34. In the case of ambiguous assignments, all hydrogens should be selected by using a wildcard specification; e.g.,

resid 34 and name HB*

selects all protons that are bonded to $C^{\beta}$ (see also the next section). The second statement selects the second atom (or set of atoms).

The file below is an example of a typical distance restraints file obtained from NOE experiments:

assign (resid  1 and name ha)   (resid  2 and name hn)   2.0 0.0 0.8

assign (resid  1 and name hg1#)  (resid 31 and name ha)   2.5 0.0 5.5
assign (resid  1 and name hg2#)  (resid 31 and name ha)   2.5 0.0 5.5

assign (resid  1 and name hg1#)  (resid 31 and name hb1)  2.3 0.0 7.3
assign (resid  1 and name hg2#)  (resid 31 and name hb1)  2.3 0.0 7.3
assign (resid  1 and name hg1#)  (resid 31 and name hb2)  2.3 0.0 7.3
assign (resid  1 and name hg2#)  (resid 31 and name hb2)  2.3 0.0 7.3

The interpretation of the real numbers is dependent on the particular restraining function used (see Section 20.3).

For distance symmetry restraints, 3D NOE-NOE restraints, and high dimensional restraints, multiple ASSIgn statements can be grouped together. For example, distance symmetry restraints are specified by

class sy
  assign (resid 1 and segid A) (resid 30 and segid B) 0.5 0.1 0.1
  assign (resid 1 and segid B) (resid 30 and segid A) 0 0 0 
potential sy symm

Xplor-NIH 2024-09-13