[phenixbb] how to define a molecule in two rigid_body

CPMAS Chen cpmasmit at gmail.com
Sat May 5 06:39:55 PDT 2012

Thanks, Ralf.

I am almost at final stage. but the refinement always shows error density
at the single bond connecting the two rings. I have tried manually change
the orientation of these two rings, but there are two concerns that I
thought why I did not get the perfect fitting.
1. I might not choose the perfect the orientation of these rings, and these
give me a non-perfect fitting, and high b-factor.
2. since phenix always tries to change the conformation a little bit to fit
the density, so this also might cause some errors, or not the conformation
I like.

Then, my sense is that, if I can somehow define the two parts of the
molecule as two rigid bodies, then phenix only can has free rotation of
these two rings, and the fitting might come out good.


 University of Pittsburgh School of Medicine

 Department of Aneshesiology
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