diao at HIS.SB.FSU.EDU
Tue Jan 6 16:58:22 EST 1998
I am refining a structure including a sulfate group.
I'd like to know the accurate occupancy of this sulfate group.
What I have done is as follows:
1. After I almost finish the refinement of this structure currently including
protein atoms, water molecules and a sulfate group, I reset all atoms b
factors to 15A^2.
2. Use brefinement.inp to refine all individual atoms thermal factors with
the sulfate group occupancy as 1.00
3. Fix all atoms b-factors except those of the sulfate group. Use bgroup.inp to
refine only the occupancies and b-factors of the sulfate group
4. Use the obtained occupancies of the sulfate group from step 3 to refine all
individual atoms thermal factors. After iterating
step 2 and 3 several times, I have found the occpancies and b factors of the
sulfate group both decrease since the occupancies are coupled with the b
factors, for example, in the beginning, q=1.0 b=48A^2, in the end, q=0.97
5. I have ever noticed that if I iterate the step 2 and step 3 alternatively,
it seems the values of the occupancies and b factors will always go down
together without convergement.
My questions: 1. How can I get the accurate evaluation for the ocupancies of
2. Should I do iterating process? Maybe I should just regard the values
output from the first round of step 3 refinement as what I need ?
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