SHELXL program

G.M. Sheldrick, SHELXL, Program for crystal structure refinement. University of Gottingen, Germany 1999. 

SHELXL Program for Structure Refinement G. M. Sheldrick, University of Gottingen (1993). 

Sheldrick, G.M. (1997) SHELXL-97, Program for Crystal Structure Refinement, University of Gottingen, Germany, Windows version by McArdle by National University of Ireland, Galway, Ireland. 

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

Sheldrick, G. M. (1997). SHELXL-97. A computer program for the Refinement of Crystal Structures. University of Gdttigen, Germany. 

After merging of the single zones, data sets of approx. 100-300 independent reflections can be obtained as described in chapter 2.5. In a first step a kinematical structure refinement should be performed using the program SHELXL [13]. The temperature factors for FAPPO were chosen as U = 0.06 for C, N and O as U = 0.10 for H atoms apart from H atoms situated at N with U = 0.12 A (Electron scattering factors [20]). To prevent the molecules from being distorted a refinement, where the whole molecule was kept rigid, was performed. This also improves the usually bad parameter/reflection ratio. In the case of modification I we obtained R-values of 31% (481 unique reflections with I > 2cr) for the 100 kV data and of 25% (385 unique reflections with I > 2a). The sparse 100 kV data of modification II was not analysed quantitatively. From 300 kV data we obtained an R-value of 23% (226 unique reflections with I > 2a). 

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... 

G. M. Sheldrick, Phase annealing in SHELXS-90 direct methods for larger structures, Acta Cryst. A46, 467 (1990) G. M. Sheldrick, SHELXL-97. University of Gottingen, Germany, (1997). See the footnote on page 515 on how to obtain the programs. 

Le Bail or Pawley extracted list of intensities with single crystal software such as Shelxl or Crystals to perform early cycles of refinement to find missing atoms, and graphically examine the structure. This is also an area where it might be helpful to Armel Le Bail s Overlap program (listed in Table 17.16) to remove reflections that are excessively overlapped. 

SHELXL is part of the SHELX program suite, a software package containing the following programs ... 

There is a commercial twin to the SHELX suite The SHELXTL package as sold by Bruker AXS contains the programs XS (SHELXS), XM (SHELXD), XL (SHELXL), XH (SHELXH), XCIE (CIETAB like), XPRO (SHELXPRO), XWAT (SHELXWAT), and some additional programs by George Sheldrick— XP... 

A critical point in this process is the evaluation of the model, as the model should only be altered if a change improves its quality. There are several mathematical approaches to define a function which is assumed to possess a minimum for the best possible model in the world of small molecules (typically less than 2(X) independent atoms) the least-squares approach is by far the most common method, while for protein structures other methods Ufce maximum likelihood have also been employed. The program SHELXL, on which this book focuses, is predominantly a program for small-molecule structures and the least-squares refinement is the only method on which we need to concentrate. The concept is simple by means of Fourier transformation, a complete set of structure factors is calculated from the atomic model. The calculated intensities are then compared with the measured intensities, and the best model is that which minimizes M ... 

In SHELXL, restraints are applied by adding a command with appropriate keywords and/or atom names in the. ins file. Even though the SHELXL reference manual, which is included as a. pdf file on the CD-ROM that accompanies this book, exhaustively elaborates on all restraints, the following pages briefly describe the most common restraints as they are used by this program. 

SHELXL calculates a least-squares plane through the first na atoms of the named atoms. The equation of this plane, together with the deviations of all named atoms from the plane and the angle to the previous least-squares plane (if present) are written into the. 1st file. If na is not specified, the program fits the plane through all named atoms. 

For the refinement of an obverse/reverse twin SHELXL needs a special reflection file in HKLF 5 format and the refinement is not possible with a single TWIN command (see the two examples in 7.8.3 and 7.8.4). This restriction is unnecessary and will be removed if and when there is a new release of the program. After producing the HKLF5 format file further merging of equivalent reflections is not possible. Therefore the data should be merged before producing this file. Otherwise all data would be treated as independent, which leads to mathematically incorrect standard uncertainties. 

After a transition from a different refinement program to SHELXL, the 5-values are different from what you had before. This can be caused by differences in the model, for example the use of different bulk solvent corrections or by different sets of reflections used for the calculation of the 5-values. In particular, the use of different sigma-cutoffs (e.g. the exclusion of reflections that have an an litude of less than say 3 times their standard deviation, f < 3a (F) ) will result in different statistics. Checking the exact number of reflections will reveal this problem and others such as different implicit resolution cut-offs. 

The list of highest peaks in a (IFo - IFc) difference density map (search for Q1 in the Ist-file) The PLAN instruction (e.g. plan 2 0 0 -1 0. l) will include the highest peaks into the pdb-file written by SHELXL to be conveniently located when the model is displayed. The positions of these peaks can also be identihed in graphics programs by performing a peak search in the appropriate electron density map. 

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