The Starting Model

The starting model is the set of coordinates that is input to the minimization program and defines the approximate geometry of the conformation and configu- 

Starting models can be derived from crystal structures of related molecules, from structures optimized with quantum hemical methods, or they can be constructed with a graphics program. 

Examples of programs that enable molecules to be constructed graphically are given in Appendix 3. 

The program used in this tutorial is Momec3, and this allows the construction of molecules, including metal complexes, without restriction with respect to coordination numbers and coordination geometries. 

There is a strong correlation between the parameters of different potential energy functions so that they should not be developed or refined in isolation. For example, the barrier to rotation about a bond can be modified by changing the explicit torsion angle term or by changing the non-bonded interactions. Thus, the effect of any change on a force-field parameter needs to be tested extensively that is, some other 

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Structure refinement is not simply the last step of solving a structure, but it is also a whole independent world on its own. On the one hand, refinement can be done on a structure which is assumed (known) from a source different from that outlined above. On the other hand, refinement is not simply a procedure resulting more accurate atomic coordinates, but also a way to verify the starting model. The model can only be accepted with high probability if it can be refined to a good match between measured and computed patterns. 

With this option (the -1 option in the MM2 manual), the residues of the starting model are rotated rigidly (without internal change) to the first < ), P combination to be considered. After the first optimization finishes, the first torsion angle specified (eg. 

Figure 5. a) The starting model of cellobiose (gtgtRR) after rigid rotation to -80, 0 -100. b) The result of attenpted optimization by MM2, c) The same linkage conformation, but the structure was taken from the study that produced the map in Figure 4. 

The Strategy conveyed in this paper permits coherent results from an automated CA while using flexible residues. By testing all the starting models over the entire range of < ) and P, parallel sets of data were obtained that were submitted to a simple program for final analysis. This minimizes the personal time required to produce a... 

The starting model at each point that gave the lowest gtgtRR, 2 gtgtCC, 3 - ggggRC and 4 - ggggRR). 

Yokouchi et al (2) used conformational energy calculations, revealing six low-energy conformations. Each of these was placed in the unit cell with the chain axis coincident with the c-axis and rotated about this axis to minimise the R-factor. One of them gave a much lower R-factor than the others, and this was chosen as the starting model. 

A surprising feature is the significant contribution to the variability of some parameters caused by differences in the starting models. This might be expected if they differed widely, but in this case the published structure of each author was used and all three were fairly close (see Table I). The point at which a... 

This method requires only a crude structural model as a starting model. In this analysis, the starting model was a homogeneous spherical shell density for the carbon cage. As for the temperature factors of all atoms, an isotropic harmonic model was used an isotropic Gaussian distribution is presumed for a La atom in the starting model. Then, the radius of the C82 sphere was refined as structural parameter in the Rietveld refinement. 

Subsequently, the baboon a-lactalbumin structure was refined at 1.7-A resolution by Acharya et al. (1989). Using the structure of domestic hen egg white lysozyme as the starting model, preliminary refinement was made using heavily constrained least-squares minimization in reciprocal space. Further refinement was made using stereochemical restraints at 1.7-A resolution to a conventional crystallographic residual of 0.22 for 1141 protein atoms. 

Only fragmentary and semiqualitative calculations have been published using this line of approach.In the work of Bylander and Rehr, the starting model is a crystal with one orbital per site described by a tight-bind-... 

Simulated annealing A structure determination from diffraction data involves the development of an initial model, that is a structure solution step, and then completion and refinement of the model. Why are these steps distinct The answer is that today s structure refinement technology can operate effectively only when the starting model is relatively dose to the actual model crystallographic least squares techniques are unable to locate global... 

The starting model of the crystal structure with all of the necessary parameters is found on the CD in files Ch7Ex05a.exp and Ch7Ex05a.cif the experimental pattern is located in the file Ch7Ex05 CuKa.raw. ... 

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