RE: [ccp4bb]: MR

["James Naismith" <naismith@st-andrews.ac.uk>]

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We have found BEAST from Randy Read to find solutions when we all but lost
hope!

If you want to go down the random search method. A simple automated method
would be work out the rotations & translation to take your zincs to lie
along one axis (put a couple of points along this line and AMORE will do
this during it centre of mass). The simply apply an incremental rotation
around the axis (5 degrees around z if you do AMORE), ie cycle = 0,
cycle_now=cycle + 1, rot_now=cycle_now x 5, in lsqkab apply rot_now to your
centred model (which has had the same centre of mass centering rot & trans
as the zinc atoms in a line applied). The add another lsqkab which would
return the zinc atom line back to the correct position, this will move your
model to a point in the cell rotated around the two zinc atoms. You can then
test the model by some criteria (I would think packing first), then test it
by calculating R-factors or correlation coeffs. The longest part of the
whole business will be writing the script. My experience is that it almost
never works (partly because I only do stuff like this when things are
hopeless) but its very satisfying to get the script running. I would use
BEAST or do phased translation searches.

best
Jim



James H. Naismith                | Research mailto:naismith@st-and.ac.uk
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