Questions and problems?

NMR

I 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 -1/6 effective distance using the IGR1, IGR2 and IR6 options of SANDER. My question is: What sort of distance corrections to the upper bound proton-proton distance restraints derived from the NOE cross-peaks are required in this case?. I presume that are not the same used in the case of employing pseudoatoms.

You do have to make corrections to the distance bounds, usually assuming a "worst-case" geometry: i.e. to find the -weighted distance that would just fit inside the (assumed) original bound.

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

Web Masters <webadmin@www.amber.ucsf.edu>

Last modified: Wed Jun 14 14:18:55 PDT 1995