puius at aecom.yu.edu
Thu Jan 8 10:40:33 EST 1998
Diao Jia-Sheng wrote:
> 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:
> 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.
As you mentioned, they're really correlated.
> My questions: 1. How can I get the accurate evaluation for the ocupancies of
> sulfate group?
Do you have a reason to believe the sulfate group does not have an occupancy of
~1.0?If you assume q=1.0, does the system behave happily? With the typical
protein crystallographic data, you may as well shave with Occam's Razor; if
the simplest hypothesis is q=1.0 with sensible B-factors, I'd stick with that,
BTW, is the sulfate on a special position or anything? That probably wouldn't
refine too well in any case.
> 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 ?
I have done something similar once. I had two ligands bound to a protein in
exclusive modes. I basically did grouped occupancy refinement of both ligands,
re-set the occupancies to sum to 1.0, and then did *individual atom* B refinement.
Because of the constraint for the occupancy sums to be 1.0, plus the fact the data
was 1.9A resolution, it converged well. If I didn't reset the occupancies to sum
to 1 each time, though, they would both move to funny values after a while --
they actually tended to run a little high.
So I think the iterative approach is fine, but if there's no reason to use it,
simpler and let q=1.0.
Yoram A. Puius Albert Einstein College of Medicine
6th year M.D.-Ph.D. Department of Biochemistry
mailto:puius at aecom.yu.edu 1300 Morris Park Avenue, Bronx, NY 10461
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