NAME
checkspider - read and check a spider 2D and 3D image file
SYNOPSIS
checkspider [ options ] spifile
DESCRIPTION
Read the spider image file spifile, determine the minimum and maximum values, the average and the standard deviation. If the spider file contains these statistics they are also printed along with the calculated values. This provides a confirmation that the data had been read correctly.All the statistics are written to the standard error output.
The options are:
-v Lv: specify the voxel length to be Lv Å. The preset value is 1.0Å. Voxels are assumed to be perfect cubes. This value should be specified if the -spider, -topvalues or -ribbons options are chosen.
-threshold T: Set the threshold value to T. The preset value is 0.0.
-interpolate: Interpolate the values to determine peaks. This option is useful only when used in conjunction with -topvalues or -ribbons. The current implementation uses interpolation of the second degree, i.e., a point whose value is to be determined is interpolated over three other points with known values. The procedure is asymmetrical, with the interpolation done on the x-axis first, then three more interpolations to determine the y-axis and finally nine interpolations to determine the z-axis. The interpolation is done for each interior grid point, 27 points at a time with overlap which will most likely result in duplicate peaks. Within each group of 27 points, a peak is found if a maximum is found within the 27 points and which has a value above the threshold value T.
-peaksonly: Find peaks that exceed the threshold value T. Peaks are defined as voxels where the value is higher than the values in the 26 immediate neighbors. This option is useful only when used in conjunction with -topvalues or -ribbons.
Only one of -interpolate or -peaksonly can be specified. In either case, the voxels at the edge of the lattice (i.e. non-interior voxels) are eliminated from contention.
-scale S: Set the scale to S. The preset value is 1.0. This is useful only when a new spider file is created. Every density is multiplied by S.
-trim Ltrim: Set the trimming level to Ltrim. The preset value is 0.0. Outer voxels are checked slice by slice in all three directions. Outer slices containing only values less than Ltrim can be removed and a smaller lattice can be formed. It is possible to specify a trimming level so high that the entire lattice is cut out.
-values: The values in the image file are written, one value per line, to the standard output. The output is potentially large. For example, for a 503 image, there will be 125000 numbers. The output can be redirected to a file or piped to an analysis program.
-topvalues: The (interpolated) positions and values that exceed the threshold T are written to the standard output. Each line contains the x, y, and z-coordinate and the density.
-ribbons RIB: write files for the Ribbons package using RIB as a file name prefix. Five files will be created named RIB.sph, RIB.cyl, RIB.model, RIB.bonds and RIB.atoms. The next two options must also be specified. Voxels with values above T will be shown as colored spheres of diameter Lv. The original lattice is plotted, i.e., any trimming is ignored. The voxel length must also be specified even if the preset value is perfectly acceptable.
The Ribbons feature is not meant to compete with other utilities that display electron density maps. There are very serious limitations with this feature. Be sure to specify a plotting level that is high enough that only a few hundred voxels are shown (Ribbons is really slow when there are thousands of spheres). To do that you probably need to form a histogram of the voxel values (see the example below) to determine the cutoff density. The spheres are colored to indicate four levels of densities. The colors indicating the lowest values to the highest are red, pink, cyan and blue. Another limitation of this feature is that when there are too many spheres to display the blue spheres tend to be obscured by the red.
-spider trimmed: write the scaled values in the trimmed lattice to a new spider image file trimmed. This file must not already exist. Although the new image file is written in the spider image format it may not conform strictly to the format. Some of the header data are simply copied to the new file without regard to whether the values are appropriate to the trimmed lattice. The only guarantee is that the trimmed file will be read properly in checkspider and elec2vlat. If no trimming or scaling is specified, trimmed will be an exact copy of the original image file.
-centroid: Calculate the centroid and write out the indices. The centroid is calculated two ways: weighted by all the densities and weighted by only the positive densities. In the first way, the densities are shifted so that the minimum density is zero. In the second way, only voxels with positive densities are considered in the balance. Note that indices start from 1 and are given for the untrimmed lattice.
EXAMPLE
checkspider -values spidermap | hgram -bar -guess 125000 -n 40Check the spider image file spidermap , request the values to be written and pipe them to the histogram program hgram where a bar graph display is requested with the values categorized into 40 bins.
FILES
SEE ALSO
elec2vlat
DIAGNOSTICS
BUGS
When a trimming value is set so high that the entire lattice is cut out, the check is repeated five more times unnecessarily. There is no harm done other than the time wasted.
NOTES
The -centroid option is not currently available in the public distribution.hgram is not part of the yammp package.
It takes about three minutes to analyze a file containing 903 voxels.
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