SAME Instruction
SAME s1 [0.03] s2 [0.03] atomnames
The list of atoms (which may include the symbol > meaning all intervening
non-hydrogen atoms in a forward direction, or < meaning all intervening
non-hydrogen atoms in a backward direction) is compared with the same number
of atoms which follow the SAME instruction. All bonds in the connectivity
list for which both atoms are present in the SAME list are restrained to be
the same length as those between the corresponding following atoms (with an
effective standard deviation s1). The same applies to 1-3 distances (defined
by two bonds in the connectivity list which share a common atom), with
standard deviation s2. If s2 is absent it is given the same value as s1.
s1 or s2 may be set to zero to switch off the corresponding restraints. The
program automatically sets up the n*(n-1)/2 restraint equations required when
n interatomic distances should be equal. This ensures optimum efficiency and
avoids arbitrary unequal weights. Only the minimum set of restraints needs to
be specified in the '.INS' file; redundant restraints are ignored by the
program, provided that they have the same sigma values as the unique set of
restraints. See also SADI.
The position of a SAME instruction in the input file is critical. If (say)
all the phenylalanine residues in a protein are to be restrained to have the
same 1,2 and 1,3 distances, and all have the same atom names (in the same
order!), and the same residue name (PHE), but different residue numbers, then
ONE SAME instruction suffices:
SAME_phe N > CZ
where the first atom in each phenylalanine is labeled 'N' and the last 'CZ'.
This instruction should be inserted before the first atom (N) of the phenyl-
alanine with the best geometry, because the connectivity table for this
residue will be used to define the 1,2 and 1,3 distances. This phenylalanine
does not have to be the first in the atom list. In this case it would also be
reasonable to impose local twofold symmetry for the phenyl ring, so a further
SAME instruction could be added before the beta (benzylic) carbon (CB) of the
same residue:
SAME CB CG CD2 CD1 CE2 CE1 CZ
where the order of the immediately following atoms is: CB CG CD1 CD2 CE1 CE2
CZ. Note that these two SAME restraints are all that is required, however many
PHE residues are present; the program will generate all indirectly implied 1,2
and 1,3 equal distance restraints! In this case it would also be sensible to
make the carbon atoms of the benzyl groups coplanar by a FLAT restraint.