SAME s1 [0.03] s2 [0.03] atomnamesThe 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 > CZwhere 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 phenylalanine 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 CZwhere 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.
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