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The CCP13 FibreFix program suite: semi-automated analysis of diffraction patterns from non-crystalline materials.

Rajkumar G, Al-Khayat HA, Eakins F, Knupp C, Squire JM - J Appl Crystallogr (2007)

Bottom Line: Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment.The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns.Various individual programs were written which allowed separate steps in the analysis procedure to be carried out.

View Article: PubMed Central - HTML - PubMed

ABSTRACT
The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g. cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known as FibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features of FibreFix are outlined and some of its applications are illustrated.

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Related in: MedlinePlus

(a) Fitting peak positions after estimation of the unit-cell parameters and their insertion into the ‘Cell Dialog’ box. Determination of the pattern centre, rotation, tilt and the camera length is needed first. Selecting ‘Generate’ in the ‘Cell Dialog’ box plots the predicted peaks on layer-lines and row-lines as shown here as small yellow circles. (b)–(g) Stages in the fitting of intensities using FTOREC and LSQINT. (b) is the FTOREC, quadrant-folded, image from (a), and (c) and (d) are the fitted background and original minus background from (b). (f) is the NOFIT image from LSQINT, which just fits the peak shapes and positions, but not their intensities. (g) is the final set of peak intensities fitted by LSQINT to the profiles in (f). A test of whether all is well is shown in (e), which is the sum of the fitted peaks in (g) and the background in (c). It can be compared directly with the original FTOREC image in (b).
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fig5: (a) Fitting peak positions after estimation of the unit-cell parameters and their insertion into the ‘Cell Dialog’ box. Determination of the pattern centre, rotation, tilt and the camera length is needed first. Selecting ‘Generate’ in the ‘Cell Dialog’ box plots the predicted peaks on layer-lines and row-lines as shown here as small yellow circles. (b)–(g) Stages in the fitting of intensities using FTOREC and LSQINT. (b) is the FTOREC, quadrant-folded, image from (a), and (c) and (d) are the fitted background and original minus background from (b). (f) is the NOFIT image from LSQINT, which just fits the peak shapes and positions, but not their intensities. (g) is the final set of peak intensities fitted by LSQINT to the profiles in (f). A test of whether all is well is shown in (e), which is the sum of the fitted peaks in (g) and the background in (c). It can be compared directly with the original FTOREC image in (b).

Mentions: In the case of diffraction patterns with preferred orientation, especially those from polycrystalline fibres, XFIX can be used to estimate the size and shape of the unit cell (Fig. 5 ▶). In order to do this computation and to plot the predicted points correctly, it is necessary for the pattern centre and rotation to have been determined. In addition, in the case of a tilted fibre, it is also necessary to provide an estimate of the specimen tilt. A uniaxially oriented system tilted to the beam will give a pattern which is asymmetrical top to bottom (assuming the fibre axis is ‘vertical’). The degree of tilt can be assessed under XFIX by using ‘Get Points’ to select four equivalent reflections, and then using the ‘Estimate Tilt’ option. Once this has been done, the expected peak positions can be plotted on the pattern using the ‘Cells’ dialogue box under the ‘Edit’ drop-down menu. Here the estimated unit-cell parameters can be inserted as well as the space group. If the camera length has already been determined using a reflection of known spacing, or by direct measurement, and is present in the ‘Parameters’ list under ‘Edit’, then estimation of the order of magnitude of the unit cell sides is made relatively easy by inspection of the main equatorial peaks (related to a and b) and the mean layer-line spacing (related to c). The values of these spacings can be estimated by using the ‘Get Spacings’ option in XFIX where the Bragg spacing (d) of a peak is shown, as well as the real space estimates of the radial (1/R) and axial (1/Z) positions of the peak. These values appear in the text box at the bottom of the FibreFix window. With the possible unit-cell parameters determined from these measured spacings and entered into the cell dialogue box (Fig. 5 ▶ a), clicking on ‘Generate’ causes the theoretical positions of the predicted lattice peaks to be drawn onto the diffraction pattern. Because at this stage the pattern has not been remapped into reciprocal space, the plotted layer-lines and row-lines are curved (Fig. 5 ▶ a), often in complicated ways, both due to the detector being flat and to the tilt of the fibre. Plotting the predicted points in this way is usually a very sensitive indicator not only of whether the chosen lattice spacings are reasonable, but also of whether the pattern is properly centred, and the estimated rotation and tilt angles are accurate. It is therefore advisable to go through this process a few times until satisfactory results are obtained before attempting to remap the data into reciprocal space using FTOREC. Note that refinement of the unit-cell parameters can be carried out in the LSQINT process (see below).


The CCP13 FibreFix program suite: semi-automated analysis of diffraction patterns from non-crystalline materials.

Rajkumar G, Al-Khayat HA, Eakins F, Knupp C, Squire JM - J Appl Crystallogr (2007)

(a) Fitting peak positions after estimation of the unit-cell parameters and their insertion into the ‘Cell Dialog’ box. Determination of the pattern centre, rotation, tilt and the camera length is needed first. Selecting ‘Generate’ in the ‘Cell Dialog’ box plots the predicted peaks on layer-lines and row-lines as shown here as small yellow circles. (b)–(g) Stages in the fitting of intensities using FTOREC and LSQINT. (b) is the FTOREC, quadrant-folded, image from (a), and (c) and (d) are the fitted background and original minus background from (b). (f) is the NOFIT image from LSQINT, which just fits the peak shapes and positions, but not their intensities. (g) is the final set of peak intensities fitted by LSQINT to the profiles in (f). A test of whether all is well is shown in (e), which is the sum of the fitted peaks in (g) and the background in (c). It can be compared directly with the original FTOREC image in (b).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483480&req=5

fig5: (a) Fitting peak positions after estimation of the unit-cell parameters and their insertion into the ‘Cell Dialog’ box. Determination of the pattern centre, rotation, tilt and the camera length is needed first. Selecting ‘Generate’ in the ‘Cell Dialog’ box plots the predicted peaks on layer-lines and row-lines as shown here as small yellow circles. (b)–(g) Stages in the fitting of intensities using FTOREC and LSQINT. (b) is the FTOREC, quadrant-folded, image from (a), and (c) and (d) are the fitted background and original minus background from (b). (f) is the NOFIT image from LSQINT, which just fits the peak shapes and positions, but not their intensities. (g) is the final set of peak intensities fitted by LSQINT to the profiles in (f). A test of whether all is well is shown in (e), which is the sum of the fitted peaks in (g) and the background in (c). It can be compared directly with the original FTOREC image in (b).
Mentions: In the case of diffraction patterns with preferred orientation, especially those from polycrystalline fibres, XFIX can be used to estimate the size and shape of the unit cell (Fig. 5 ▶). In order to do this computation and to plot the predicted points correctly, it is necessary for the pattern centre and rotation to have been determined. In addition, in the case of a tilted fibre, it is also necessary to provide an estimate of the specimen tilt. A uniaxially oriented system tilted to the beam will give a pattern which is asymmetrical top to bottom (assuming the fibre axis is ‘vertical’). The degree of tilt can be assessed under XFIX by using ‘Get Points’ to select four equivalent reflections, and then using the ‘Estimate Tilt’ option. Once this has been done, the expected peak positions can be plotted on the pattern using the ‘Cells’ dialogue box under the ‘Edit’ drop-down menu. Here the estimated unit-cell parameters can be inserted as well as the space group. If the camera length has already been determined using a reflection of known spacing, or by direct measurement, and is present in the ‘Parameters’ list under ‘Edit’, then estimation of the order of magnitude of the unit cell sides is made relatively easy by inspection of the main equatorial peaks (related to a and b) and the mean layer-line spacing (related to c). The values of these spacings can be estimated by using the ‘Get Spacings’ option in XFIX where the Bragg spacing (d) of a peak is shown, as well as the real space estimates of the radial (1/R) and axial (1/Z) positions of the peak. These values appear in the text box at the bottom of the FibreFix window. With the possible unit-cell parameters determined from these measured spacings and entered into the cell dialogue box (Fig. 5 ▶ a), clicking on ‘Generate’ causes the theoretical positions of the predicted lattice peaks to be drawn onto the diffraction pattern. Because at this stage the pattern has not been remapped into reciprocal space, the plotted layer-lines and row-lines are curved (Fig. 5 ▶ a), often in complicated ways, both due to the detector being flat and to the tilt of the fibre. Plotting the predicted points in this way is usually a very sensitive indicator not only of whether the chosen lattice spacings are reasonable, but also of whether the pattern is properly centred, and the estimated rotation and tilt angles are accurate. It is therefore advisable to go through this process a few times until satisfactory results are obtained before attempting to remap the data into reciprocal space using FTOREC. Note that refinement of the unit-cell parameters can be carried out in the LSQINT process (see below).

Bottom Line: Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment.The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns.Various individual programs were written which allowed separate steps in the analysis procedure to be carried out.

View Article: PubMed Central - HTML - PubMed

ABSTRACT
The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g. cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known as FibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features of FibreFix are outlined and some of its applications are illustrated.

No MeSH data available.


Related in: MedlinePlus