REFIN program

First, the structure should explain the data. Apart from the energy or target function value returned by the refinement program, this check can be performed with some independent programs (e.g., AQUA/PROCHECK-NMR [90], MOLMOL [91]). The analysis of the deviations from the restraints used in calculating the structures is very useful in the process of assigning the NOE peaks and refining the restraint list. As indicators of the quality of the final structure they are less powerful, because violations have been checked and probably removed. A recent statistical survey of the quality of NMR structures found weak correlations between deviations from NMR restraints and other indicators of structure quality [88]. 

In this chapter, the structure refinement program will be used to determine the structural parameters of graphitic carbons as shown in section 3. 

The structure refinement program for disordered carbons, which was recently developed by Shi et al [14,15] is ideally suited to studies of the powder diffraction patterns of graphitic carbons. By performing a least squares fit between the measured diffraction pattern and a theoretical calculation, parameters of the model structure are optimized. For graphitic carbon, the structure is well described by the two-layer model which was carefully described in section 2.1.3. 

Figure 6 shows the changes which occur in the diffraction patterns of the heated MCMB samples, and the excellent description of these patterns by the structure refinement program. The structural parameters, P, P, a, doo2> Lc the carbon samples are listed in Table 1 [6]. 

Fig. 6. The X-ray diffraction patterns and calculated best fits from the structure refinement program for the samples MCMB2300, iVICMB2600 and iVfCMB2800.

Foster Wheeler Environmental Corporation. 1995. Feasibility Study, Soil Volume refinement program, geotechnical sampling in the new toxic storage yard, section 31, Rocky Mountain Arsenal. Final Report. Version 2.0. 

SHELXL [28] is the most commonly used structure refinement program. We have devised a strategy for addressing the refinement ... 

Ragazzi, M./ Ferro, D. R. REFINE , Program and user s manual available on request. 

Unfortunately, the relations between the electron density, the restraints we have discussed here, and the structure factors are non-linear. Thus, the only strategy we can adopt is to use the approximate phases we start out with and improve these iteratively. Even this is not straightforward, mainly because Eq. 1 is expensive to compute. However, there exists a powerful and straightforward procedure that is used in virtually all phase refinement programs Eourier cycling. 

Macromolecular crystallographic refinement is an example of a restrained optimization problem. Standard refinement programs adjust the atomic positions and, typically, also their atomic displacement parameters of a given model with the... 

One of the most popular refinement programs is the state-of-the-art package Refmac (Murshudov et ah, 1997). Refmac uses atomic parameters (xyz, B, occ) but also offers optimization of TLS and anisotropic displacement parameters. The objective function is a maximum likelihood derived residual that is available for structure factor amplitudes but can also include experimental phase information. Refmac boasts a sparse-matrix approximation to the normal matrix and also full matrix calculation. The program is extremely fast, very robust, and is capable of delivering excellent results over a wide range of resolutions. 

SHELXL (Sheldrick and Schneider, 1997) is often viewed as a refinement program for high-resolution data only. Although it undoubtedly offers features needed for that resolution regime (optimization of anisotropic temperature factors, occupancy refinement, full matrix least squares to obtain standard deviations from the inverse Hessian matrix, flexible definitions for NCS, easiness to describe partially... 

Tronrud, D. E., Ten Eyck, L. F. and Matthews, B. W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallogr. A 43,489-501. 

Dihedrals are not generally constrained to expected values in refinement programs. Any... 

XPLOR is a modern package of refinement programs that includes powerful procedures for energy refinement by simulated annealing, in addition to more traditional tools like least-squares methods and molecular-replacement searches. The package is available for use on many different computer systems. Simulated annealing for large molecules usually requires supercomputers. 

In the last few years rapid advances have been made in the field of computational crystallography, so that it is now possible to produce highly refined computer models of a wide variety of polymeric materials using X-ray diffraction data. Unfortunately, these achievements have been negated to some extent because the techniques used to collect the data for such refinement programs have not advanced at a comparable rate. In this contribution we describe a computer program which facilitates the reduction of intensity and d-spacing data obtained by the multiple film-pack method, and attempts to quantify the errors associated with such measurements. 

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