The SDA robot (Scratchuator) demonstrates the potential for low cost nanometer positioning of chip sized components for alignment and flip chip assembly as well as precision sample positioning for surface analysis.
The main operating units described there are seen as being the primary components of "value". Alignment thinking requires all decision makers to view their enterprise as a value chain, not merely a set of more or less valuable boxes and wires on an easy-to-forget, ever-changing chart.
The Lagrangian multipliers can be expressed as functions of dislocation moments M k) which we define as the first components of the alignment tensors in the rotated coordinates: (M^{ k)}:=rho ^{prime }^{ k)}_{1ldots 1}=rho ^{ k)}_{1ldots 1}({varphi }-{varphi }_{boldsymbol {rho }})).
These criteria were applied pairwise to the human/mouse, human/macaque, and mouse/rat components of every alignment.
Initial values of the axial (Da) and rhombic (R) components of the alignment tensor were estimated from a histogram of RDC distribution, and final optimized Da and R values were obtained by iterative fitting of the measured RDCs to the preliminary structure using PALES (33).
The axial and rhombic components of the alignment tensor were explored with MODULE 1.0 and a grid search procedure to obtain reliable values of Da and R. The grid search was repeated using RDC values from the SLIds2 stem (residues 1 6, 16 21) and the SLV stem (residues 2 7, 15 20), independently.
For this reason, in our recent study [ 2, 3], we combined NCFs and ASs of MI-GRAAL [ 7] and IsoRankN [ 24], two state-of-the-art methods at the time, as a proof of concept that it is important to fairly evaluate the contribution of each component to alignment quality.
The anchoring approach that we implemented can help to find out which component of our alignment program is to blame if automatically produced alignments are biologically incorrect.
The magnitude of the principal component of the alignment tensor, DaNH, is 5.6 Hz and the rhombicity is 0.3.
In this work, we attempt to add a component of flexible alignment in local variable regions which are initially recognized by rigid body superposition.
For the structure component of the alignment, we used BRCA1 RING NMR structure 1JM7.pdb and the BRCA1 BRCT repeat crystal structures 1JNX.pdb and 1T29.pdb [ 28- 30].
