Automatic Model Building

Dowler, C. A. Automatic Model Building Cuts Design Time, Costs. Plastics Engineering, pp. 43-45, Apr. 1989. 

This paper describes the first application of analogy and intelligence to molecular model building. It represents a departure from previous methods, a new approach aimed at rapid, automatic, accurate molecular model building. 

High resolution (between 1.4 and 2.0 A) Automated model building with ARP/wARP should work with most phase sets. RESOLVE, which uses a template-based rather than atom-based approach, should also perform well but may be computationally more consuming. Refinement can best be carried out with REEMAC or PHENIX using isotropic ADPs since the amount of data is no longer sufficient for an anisotropic description of atomic displacement parameters. The use of TLS (Winn et ah, 2003) is highly recommended. A use of NCS restraints should be critically evaluated and in most cases the refinement can proceed without them. Double conformations of side chains should be visible and modelled. Ordered solvent can be modelled automatically. 

Figure 5.1 Computational model building. In this example structural elements from the Hollandite structure (highlighted in (a)) are combined (b) to produce analogue structures. Once the structural elements have been reassembled in the appropriate form, a new unit cell can be defined (either automatically or by selecting translationally related atoms) (shown in (c)) and the symmetry of the new structure, constructed from regular and symmetrical elements, automatically determined (d) (in this case the new, enlarged, model is P42/m Hollandite itself is 141m). Once a new model is constructed its properties can be readily characterized as in (e) where the calculated X-ray powder diffraction pattern of one of many alternative Hollandite derivative structures is shown.

Each of the automated techniques we have described has its own strengths and weaknesses. The 3D key approach provided within ChemDBS-SD o is attractive, because all stages of the process, from conformational analysis through model building, are handled automatically. The technique tends to produce many models, however. This is not necessarily a problem, but it does mean that more false positives will need to be weeded out during the validation... 

You start building propanal using an sp C from the model kit Note that five dif ferent types of carbon are available Each is defined by a particular number of unfilled valences (these are used to make bonds) and a particular idealized geometry Valences that are not used for bonds are automatically turned into hydrogen atoms so it is nor mally unnecessary to build hydrogens into a model... 

As an example stereolithography is a 3-D rapid process that produces automatically simple to very complex shaped models in plastic. Basically it is a method of building successive layers across sections of pho-topolymerized plastics on top of each other until all the thin printed layers can be joined together to form a whole product. The chemical key to the process, photopolymerization, is a well established technology in which a photo initiator absorbs UV energy to form free radicals that then initiate the polymerization of the liquid monomers. The degree... 

We have added a companion option to PBUILD, PRANDOM which eases considerably the problem of finding good conformations of a polymer segment. PRANDOM automatically selects all of the polymer backbone and/or side chain bonds and will randomly select rotations for each bond. In a few minutes, one can not only build a polymer fragment, but also set up a Monte-Carlo search of its conformational space. However, even this cannot solve the problems for large models (pentamer or larger), again due to the number of bonds to be rotated. 

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