On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote:
> With Garib's help, I have forced the atom into its position by using
> external distance restrains of zero length against the same
> symmetry-related atom. The cause is unclear because the same program
> handles special positions in another structure just fine.
Thanks - good to know. Perhaps a good practice is to take care of
special positions manually every time just in case.
>From what I understand, the way refinement software generally treats
special positions (other than automatically resetting occupancy to 1/z)
is to exclude vdw repulsion to symmetry-related atom which in this case
would always push the atom out of position. Exclusion is usually
applied to the atom when it is within the cutoff distance (0.1A?) from
the corresponding symmetry element. If for whatever reason the atom
shifts, the vdw will push it out. Why would such atoms shift varies - I
suspect in some cases it is due to hydrogen bonding restraints, in
others it could be due to noisy density.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
