BUMP Instruction
BUMP s [0.1] d1 [#] d2 [#] d3 [#] ...
'Antibumping' restraints are generated automatically for all (solvent water)
atoms which have been flagged with 'CONN 0'. The restraints can be generated
between CONN 0 atoms and all other non-hydrogen atoms, and appear in
subsequent tables as DFIX instructions with negative d and effective standard
deviation s. The values to be used for d are given in SFAC order as d1, d2,
d3, ...; the default values are 3.2 for C, 2.7 for N, 2.6 for O and 3.5 for
ALL other elements. If the structure contains atoms of other elements (e.g.
explicit cations in polynucleotides) that can interact with the solvent, it
will be necessary to specify the appropriate distances on the BUMP
instruction. The restraints are also set up for all symmetry equivalents
automatically; however if the sum of occupancies of the two atoms is less than
1.1, no restraint is generated. Iterative refinement with antibumping
restraints, followed by deletion of atoms which persist in giving unacceptable
distances or for which the (equivalent isotropic) displacement parameters
become larger than say 1.0 to 1.2 A^2, and insertion of new potential solvent
atoms from difference electron density syntheses, provides a reliable
procedure for building up a solvent model with acceptable hydrogen bonding
distances which is consistent with the diffraction data; 'PLAN 200 2.3' would
be appropriate. If there are more than 15 different SFAC types, d15 is used
for those with numbers greater than 15.