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[ccp4bb]: alternate conformation with ion and Cl- coordination
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The electron density near an ARG side chain suggests (beyond CB) a partially
ocupied ion site (quite round "blob" , probably Cl-, crystallization
conditions) of which one coordinant must be this ARG side chain. Nevertheless,
occupancy 1 (of the Cl- ion) in its (supposedly) position claims a little
excess of atoms (Fo-Fc); besides, there is a somehow faint (electron density)
link beyond the CB and the "blob", but at putting the ARG side chain there
(occupancy 1), there are two claims: excess atoms on the "link" and lack of
atoms on the center of the "blob" (Fo-Fc). My hypothesis: alternate conf. for
the ARG, say, 70 % and 30 % (numbers assumed to ease the discussion), in case
ARG 70 % coordinate the (70% occupancy) Cl- ion and in case the rest ARG 30 %
occupies (well its terminal atoms) the (100% - 70%) Cl- position. Is it
possible in refmac to refine this ARG alternate with only the " 70 %"
conformation coordinating the CL- and the remaining 30 % ARG in the Cl-
position, I mean, the problem here is to turn off the interactions between the
Cl- and the 30 % conformation ? I read the manual but not could find how to do
that (if ever possible). (There are other coordinators for the ion which maybe
less protonated could alow the presence of the ARG threin).
Has someone ever found a similar case ? Point to literature, etc... are
welcome. Also, I found webites about coordination of metals. Points to sites
or articles about coordination of anions, specially Cl- are welcome also.