The scale bars used in the experiment were finely precalibrated to be 30″ and were used to convert the relative orientation to absolute units (Figure 7).
In addition, a novel paramagnetic relaxation enhancement experiment using a spin-labeled ligand analogue, 5'-diphospho-4-O 2,2,6,6-tetramethylpiperidine 1-oxyl (UDP–TEMPO), was used to characterize the relative orientation of the two bound ligands.
Using this integrated visualization tool, we performed three important types of manual improvements to the stage I PMs: (1) scaffolding links were used to provide the relative orientation of superscaffolds, (2) adjacent superscaffolds not previously included in the integrated genetic/physical map were added, and (3) errors in the assembly were identified.
Yaw, pitch, and roll all measured by the magnetic sensor are used to describe the relative orientation between the world and eye coordinate systems (Figure 4).
The elbow angle, which is commonly used to describe the relative orientation of the variable versus the constant domains of each Fab fragment, differed significantly between the two 7C8 molecules present in the asymmetric unit with 138° and 184° for 7C8 monomer 1 (chains A and B) and monomer 2 (chains H and L), respectively (Figure 1C).
It was soon demonstrated that RDCs can be used to determine the relative orientation of domains in multidomain proteins.
As these chromosome assemblies have been constructed partly by using the S. cerevisiae genome to orient and order scaffolds, alignments were also made to the unordered scaffolds using MUMmer [ 49] to confirm the relative orientation of chromosomal segments inverted between species.
A 3D solution structure model of the reduced form of the cytochrome has been determined using NMR data in order to determine the relative orientation of the haems.
Thus, using Strand-seq and BAIT with relatively low-coverage sequencing, the relative orientation of all reference contigs can be determined, effectively bridging all gaps in an assembly.
FTDOCK was used to scan the relative orientations of the molecular complex in a systematic way, and produced 10,000 docking orientations.
