Composite omit maps CNS 1.0

Mitchell Guss M.Guss at biochem.usyd.edu.au
Mon May 8 00:30:57 EST 2000


In version 1.0 of CNS the script "composite_omit_map.com" requests a
percentage volume to be omitted and cautions that this should be less
than 10%.  If I understand the script correctly, the total volume is
calculated from the "volume" of atoms in the model (= no. of atoms *
9).  The length of the side of the omitted box is then given by the cube
root of the "specified percentage to be omitted" of the total volume.

In a case where there is a very large solvent content (80%) and one
specifies a volume of 10% to be omitted, the result is that the  box
size is about 1% of the asymmetric unit volume and the number of
dynamics cycles is very large and the total job runs for a long time.

Does anyone have any comments about the merits or otherwise of
calculating the omitted volume in this way rather than simply a fixed
percentage of the volume of the asymmetric unit?  An earlier version of
CNS (or perhaps it was X-PLOR) requested the length of the side of the
box to be omitted.

Mitchell Guss





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