Hi everyone:
I seem to not have when I try to refine occupancies and
alternate positions of my substrate. I have a pyrophosphate
with the configuration of one side may be a key factor,
but it's in 2 configurations in the active site. I can't
figure out how to allow _only_ one -PO3 group to vary.
q_group.inp summary & problem:
------------------------------
I couldn't figure out how to make 2 -PO3 groups for one
side of the PPi that would work in q_group, so I made
2 PPi's with the one side equiv for both PPi's. Then I
ran q_group.inp to refine occupancies. This seemed to
work somewhat, but I can't figure out how to restrict
the occupancies of alternate configurations to be = 1.00.
anneal.inp summary & problem:
-----------------------------
I normalized the alternate configurations and edited the
q_group.pdb output, and went on to anneal.inp. anneal.inp
tells me that the atoms in the alternate configurations of
PPi are too close, and proceeds to attempt to refine them
away from one another.... one goes off into the solvent.
I suspect that the .pdb input format is not correct, but
I see no examples of correct formats in the tutorial. I
also see no examples of refining alternate configurations.
Can anyone help me out?
thanks
diane
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diane h peapus, phd dp72 at cornell.edu
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