U.S. flag

An official website of the United States government
  next up previous contents index  Xplor-NIH home Documentation

Next: Syntax - SANI Up: XPLOR Interface Manual Previous: Requirements


Residual Dipolar Couplings

Partial orientation of macromolecules in solution has allowed the detection of residual dipolar couplings (RDCs). The use of an external orientational axis is necessary to compute the potential. There are a few implementations of the potential. SANI is for dipolar coupling between atoms that are directly bonded. XDIP is more flexible and can handle $^1$H-$^1$H dipolar couplings with fixed or varying distances. VEAN (VEctor ANgles) uses $N$ residual dipolar couplings converted into $N*(N-1)/2$ intervector angles. TENSO allows the rhombicity and amplitude of the alignment tensor to be calculated from the structure. Neither VEAN nor TENSO utilize an orientational axis. ANIS is a generic angular potential and can be used to test out new orientational potentials.

The dipolar coupling $D$ is defined as

\begin{displaymath} D=D_a (3\cos^2 \theta -1) + \frac{3}{2}R( \sin^2 \theta \cos 2\phi), \end{displaymath} (28.1)

where $\theta$ is the angle between the internuclear vector and the $z$ axis of the tensor, and $\phi$ is the angle between the projection of the internuclear vector on the $x-y$ plane of the tensor and the $x$ axis.

The energy term (for SANI) is $E_{RDC}=K_{RDC} (D_{calc}-D_{obs})^2$.

References for SANI include Tjandra et al. (1997b), Clore, Gronenborn, and Tjandra (1998), Clore, Gronenborn, and Bax (1998) and Clore et al. (1999). References for XDIP include Tjandra, Marquardt, and Clore (2000). The reference for VEAN is Meiler et al. (2000). The reference for TENSO is Sass et al. (2001). A good general reference for the use of RDCs in structure determination can be found in Bax, Kontaxis and Tjandra (2001).


Subsections
next up previous contents index
Next: Syntax - SANI Up: XPLOR Interface Manual Previous: Requirements   Contents   Index
Xplor-NIH 2024-09-13