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Special positions

Gerard 'CD' Kleywegt GERARD at XRAY.BMC.UU.SE
Fri Feb 16 12:19:29 EST 1996

you can check this easily from the output:

 XRFILL: #scatt.= 1169 #anomalous=  0 #special pos.=  3 occupancies=1

i would guess this doesn't change once xplor realises at startup
time that some atoms are in special positions, but i'm not sure

as to how close: close
simple trick to get close enough coordinates:
centre on the special pos atom in O; use symm_sphere
to get all other symmetry-related positions (only
one if it is a twofold); average the coordinates
of the atom + all symmetry mates
i think this should give you the position on the N-fold

to specify special positions, i tend to use a little
"include file" ("special.xplor"), e.g.:

{ special.xplor - exclude interactions with atoms in special positions }
{ define special atoms }
{ 800-801 = waters on a 3-fold }
{ 900 = phosphate on a 3-fold }
 vector ident ( store1 ) ( resid 800 or resid 801 or resid 900 )
   INTERaction ( not ( store1 ) ) ( all )
      weights * 1. end
   INTERACTIOn ( store1 ) ( all )
       weights * 1. pvdw 0. pele 0. end

also use wmin=0.1 in the parameter nbonds statement to prevent
listings of "bad" contacts

finally, you may want to fix atoms in special positions
to prevent them from drifting, or use harmonic restraints
to keep them in place; this is probably not necessary for
big scatterers but might be useful for waters


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