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Department of Chemistry and Chemical Biology |
Questions and problems?NMRI am using SANDER to refine the structure of a protein using NMR derived restraints. For distance restraints involving equivalent and nonstereospecifically assigned protons, I incorporate the
You do have to make corrections to the distance bounds, usually assuming
a "worst-case" geometry: i.e. to find the
I don't know that this is well-described in the literature (although it
probably is and I have missed it). You can see how AMBER does it by
looking at the "rm6" routine in "makeDIST_RST.c" (in the version 4.1
distribtuion in src/nmr_aux/prepare_input). Note that SANDER does not do
this sort of correction automatically: you need to run makeDIST_RST or
some other equivalent algorithm to get the "corrected" distance bounds.
[Also note that in most cases, the corrections are very modest: they increase
the bound by a few tenths of angstrom, generally by less than the uncertainty
in the bound itself.]
Dave Case
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