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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 25.2, pp. 704-705
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To facilitate visual evaluation of phasing results and input data, several (mainly interactive) programs are provided within the package. The programs are used to display contoured electron-density or Patterson maps, for interactive editing of solvent or averaging masks, and for visualization of input or difference diffraction data on workstation monitors or terminals. In most instances, hard copies for inclusion in manuscripts are also obtainable. The interactive graphics programs MAPVIEW, PRECESS and VIEWPLT are provided with two versions of each: one for use on Silicon Graphics workstations and the other (indicated by the same program name but ending in _X) for use on any display device supporting the X-Window protocol. The functionality, input and documentation are identical in both versions of each program.
The interactive program PRECESS is provided to display diffraction data in the form of pseudo-precession photographs. One can display any zone or step through all zones, with the corresponding intensities mapped to a colour scheme. If a grey scale is selected, the image looks very much like a properly exposed precession photograph taken with Polaroid film. When the cursor is placed near a reciprocal-lattice point, the Miller indices, intensity, standard deviation and d spacing are displayed, allowing one to quickly confirm or identify space groups and Laue symmetry. If a scaled file is input containing isomorphous-replacement or anomalous-scattering data, one can display the corresponding intensity differences instead of the native intensities and quickly visualize the distribution of differences to help assess isomorphism.
The interactive program MAPVIEW can be used to examine contoured electron-density or Patterson maps, as well as to examine, create or edit solvent or averaging masks. Either full-cell FSFOUR maps or submaps (including skewed submaps) can be used, although only from the former can any arbitrary region be obtained and reordered interactively. The mask creation and editing functions have been described earlier. The program is very useful for Patterson analysis, evaluation of phasing results and to help decide which region is appropriate for isolating a molecule for use in model building. It is usually crucial for construction of averaging masks, but is also useful for examining or editing other masks.
While MAPVIEW is extremely useful, there are times when it is desirable to have individual plots available either for comparison, stereo viewing of electron density, or incorporation into documents. The program CTOUR (batch) handles these functions and accepts an input FSFOUR map or submap. The CTOUR program can create any number of plot files in a single run, with each consisting of either an individual section, a mono projection, or a stereo projection, with each projection over different multiple sections. If full-cell FSFOUR maps are input, any desired region may be selected, whereas if submaps (including skewed maps) are input, the accessible regions are limited by those present in the input map.
The plot files created by CTOUR are generic in nature and are not directly displayable. One needs a driver program to convert the generic files to the format appropriate for the desired display device. The appropriate drivers for several popular display devices are provided within the package and are described below.
For display on Silicon Graphics workstations, the interactive program VIEWPLT can be used to examine the generic plots created by CTOUR. Up to ten plots can be displayed simultaneously. It is particularly useful to display the various contoured Harker sections simultaneously during difference-Patterson interpretation.
For display of CTOUR plots on monitors supporting the X-Window protocol, including most workstation monitors and X-terminals, the program VIEWPLT_X can be used instead of VIEWPLT. The functionality is identical to the GL version.
The interactive program MKPOST is provided to generate standard PostScript equivalents from the generic plot files produced by CTOUR. Multiple plot files can be generated in the same process. The PostScript files can be printed, viewed with a PostScript previewer, or incorporated into other documents.
