Hi,
I tried updating some old refinement scripts that use the "sani"
statement to incorporate RDC data, with fixed values of axial and
rhombic terms that we get by fitting experimental RDCs to calculated
structures in the PALES program. (I know there are better ways of
doing this these days, but I was in a hurry). PALES outputs values
that need to be corrected for the maximum dipolar couplings of a
given spin pair. I used three sets of RDCs, N-NH, C'-Ca and N-C'.
After the correction, the absolute values of A and Rh that I get for
all three sets are very similar (all obtained with the same alignment
medium, so no surprise there).
My question is, once XPLOR gets the A and Rh terms, how does it
correct for the differences in the magnitudes of the couplings when
calculating the energetics and errors? Two of the classes that I
used in defining the RDCs had arbitrary names (JNC and JCC). Only
JNH is a class that was previously defined in the script. I note
that our fits from PALES are much better than what the output of
XPLOR suggests they are; so I suspect there is some correction term
that I am missing.
Thanks,
Tom Pochapsky
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