Structure solution software

The disordering problems are discussed here based on the authors own experience and selected results. The problem is very common, however, and if it does not appear in the literature as often as it comes out in the laboratory work, it is simply because the authors have the tendency to skip over this kind of difficulty and chose another solvent, other conditions, etc. Let us opine that in such a way, we miss some important information on the chemical compounds we have in our hands. Structural analysis produces snapshots of molecular (supramolecular) structures, and if we are able to take snapshots of molecules in different supramolecular environment, it gives us much broader experimental experience. It is hoped that greater availability of X-ray diffraction techniques and structure solution software will not only bring a... 

Structure Solution Software Specifically for Powder Diffraction... 

Software References Included or linked structure solution software Included or linked refinement software... 

While overshadowed by dedicated powder diffraction based structure solution software, single crystal structure solution programs can still be used where a list of HKLs and intensities are available and can be usefully applied (Table 17.23). This allows not only the use of Direct Methods, but also Patterson and Patterson-based fragment searching. Armel Le Bail s Overlap program (listed in Table 17.16) can remove reflections that are excessively overlapped, sometimes aiding single crystal software based structure solution. 

For solving organic, and perhaps organometallic, it can be time saving to convert a 2D model into a 3D model suitable for input in some of the available structure solution software (Table 17.24). It is possible that the conversion may get the confirmation of the more complex molecules incorrect. Thus the user must enable the required molecular flexibility within the structure solution software. 

Table 17.22 Available powder structure solution software.

Table 17.23 Available single erystal structure solution software.

Once a structure of the desired protein has been solved, it is a very rapid process to produce subsequent high-quality structures and, in fact, some groups have even linked various scripts together, or modified software tools to provide much more automated software aids to repeated crystal structure solution, such as when solving multiple ligand complexes of the same protein [7]. 

An emerging goal in the field of macromolecular crystallography methods development is the overall automation of the time-consuming steps in structure solution. To a large extent, two software packages exemplified that concept at the turn of the previous... 

In modern crystallography virtually all structure solutions are obtained by direct methods. These procedures are based on the fact that each set of hkl planes in a crystal extends over all atomic sites. The phases of all diffraction maxima must therefore be related in a unique, but not obvious, way. Limited success towards establishing this pattern has been achieved by the use of mathematical inequalities and statistical methods to identify groups of reflections in fixed phase relationship. On incorporating these into multisolution numerical trial-and-error procedures tree structures of sufficient size to solve the complete phase problem can be constructed computationally. Software to solve even macromolecular crystal structures are now available. 

DIRDIF Beurskens Structure solution www-xtal.sci.kim.nl/xtal/documents/software/dirdif.htail... 

Various programs exist, many of which focus on specific types of phases (organics, zeolites, etc). When starting out with structure solution, the EXPO Direct Methods software can be the easiest and quickest to use. If direct... 

Structure Solution Using Single Crystal Software... 

Table 17.33 Software for crystallographic structure visualization during structure solution and refinement.

A good mailing list for advice and hints on structure solution, as well as announcements on new software updates and jobs on offer... 

We report on a project that attempts to design such quality indicators. The described software produces a reader-friendly report on all anomalies, unique features, and errors in PDB files. The magnitude of the coordinate errors can, in many cases, be assessed and, in some cases, these errors can even be corrected without the need of using the experimental structure determination data. Several aspects of structure validation will be discussed and a few examples will be worked out in detail to illustrate the possibilities and difficulties of validation. It is envisaged that the software described here will help the scientists in determining these structures to maintain the quality of their products in an environment that allows for an ever-increasing rate of structure solution. 

Powder diffraction techniques have developed enormously since 1990. This is partly due to improved X-ray and neutron sources and instrumentation and partly because of improved methods, algorithms and software for structure solution and refinements of experimental data. The more effective computers are also important. 

Finally, there has been significant progress in software and methods for structure solution and refinements during the last years. Based on the steady improvement in computer performance, it is expected that algorithms and software codes will be further improved and strengthen in the coming years. 

The process of structure solution of an unknown material from powder data can be divided into several steps. First one must record the highest-quality data possible on a (ideally) pure sample. One must then determine the unit cell parameters from observed peak positions (several software packages exist to tackle this nontrivial step). The space group symmetry must then be determined from systematic absences. At this stage, one of a number of different routes can be followed. One... 

Filippov IV, Nicklaus MC (2009) Optical structure recognition software to recover chemical information OSRA, an open source solution. J Chem Inf Model 49(3) 740-743... 

---