This procedure checks the initial R value and determines the ideal
weight 
(and 
if a phase restraint is used)
between 
and 
. The procedure
should be carried out before running
any refinement on the system. The weight 
is determined by running a
brief molecular dynamics calculation without 
and then comparing the norm of the gradient of 
and the norm of the gradient of 
.
The program will display the weight. A similar procedure should be
applied when using targets other than the crystallographic
residual (Eq. 12.1).
If the minimizer exits with ``line search abandoned" and
very large van der Waals energies (in the thousands of
kcal mole
), the
structure probably has bad contacts. The output of
X-PLOR provides a list of bad contacts
.
One should check the molecule and symmetry-related molecules on
the graphics and fix the problem. If this is inconvenient,
try the following procedure:
use the ``repel" nonbonded energy
function (see Section 4.1) for
the first several steps of minimization. One should
replace the minimization statement in the example above
with the following statements:
parameter nbonds repel=0.89 rcon=4. end end
{*This turns on the repulsive *}
{*function. *}
minimize powell
nstep=40
drop=40.0
end
{* This switches back to the Lennard-Jones function.*}
parameter nbonds repel=0.0 end end
minimize powell
nstep=40
drop=40.0
end