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Distance Symmetry Restraints
The symmetry function restrains distance differences
between pairs of ASSIgn statements. The
distance pairs should be entered as follows:
assign (segid a and resid 1 and name ca) {* First distance.*} (segid b and resid 10 and name ca) 0.0 0.1 0.1 {* Second distance.*} assign (segid a and resid 10 and name ca) (segid b and resid 1 and name ca) 0.0 0.0 0.0This particular example restrains the signed difference between the first and second distance to . The values of , , and for the second distance are not used by the program.
The list of symmetry-related intermonomer distance differences for a dimeric protein can be generated automatically by the following script, which produces a file “symrest.tbl":
{* Name of the distance restraints file.*} set display=symrest.tbl end {* Get number of residues in monomer.*} vector do (store1 = decode(resid)) (segid a and name ca) vector show min (store1) (segid a and name ca) evaluate ($first_residue = $result) vector show max (store1) (segid a and name ca) evaluate ($last_residue = $result) for $id in id (name ca and segid a) loop res1 vector show element (resid) (id $id) evaluate ($resid1 = decode($result)) evaluate ($resid2 = $last_residue - $resid1 + $first_residue) if ($resid2 > $resid1) then display ! distance pair $resid1 $resid2 display assign (resid $resid1 and name ca and segid a) display (resid $resid2 and name ca and segid b) 0 0 0 display assign (resid $resid1 and name ca and segid b) display (resid $resid2 and name ca and segid a) 0 0 0 end if end loop res1The resulting distance difference list will restrain the distance differences to 0; i.e., it will attempt to produce a perfectly symmetric arrangement of the dimer.
The next example shows how one would actually use the symmetry restraints:
noe class symm @symmetry.tbl potential symm symmetry scale symm 1.0 sqconstant symm 1.0 sqexponent symm 2 soexponent symm 1 rswitch symm 0.5 sqoffset symm 0.0 asymptote symm 1.0 endNote that these symmetry distance restraints are more stringent than the non-crystallographic symmetry restraints described in Section 18.1. The distance symmetry implies twofold symmetry whereas the non-crystallographic symmetry restraints simply restrain the monomers to be nearly superimposable without specification of a specific operation between the monomers. The distance symmetry restraints are, however, less stringent than the strict non-crystallographic symmetry (Section 18.2), as the latter requires explicit specification of the symmetry operation. The distance symmetry restraints allow the separation between the monomers to be a self-adjusting parameter. For further reading, see Nilges and Brünger (1991).
Xplor-NIH 2024-09-13