[Chimera-users] carbon-chlorine bond

Francesco Pietra chiendarret at gmail.com
Sun Nov 16 11:00:11 PST 2008

For a monochlorinated small alkaloid docked onto a protein model,
after molecular dynamics simulations Chimera shows the chlorine atom
as a dot, without a line to represent the bond. Before dynamics, the
C-Cl line connecting the two atoms was shown. Other viewers show the
bond both before and after MD.  For the purpose of presentation, how
to set a longer C-Cl bond length as a temporary default for Chimera?

Very likely the parameterization for chlorine in the MD suite is not
as it should.

francesco pietra

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