sulfate occupancy

Diao Jia-Sheng diao at HIS.SB.FSU.EDU
Tue Jan 6 16:58:22 EST 1998


Hi, All:

   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
   simutaneously.

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
   b=42A^2.

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
the
sulfate group?

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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