Email: robert.rambo@diamond.ac.uk
Tel: +44 (0)1235 56 7675
OTOKO is a 1-D interactive data manipulation package for (X,Y) data. The program is has a wide range of applications even if some of the instructions and options are specific to X-ray applications. OTOKO was originally developed in Hamburg in the 70's by P.Bendall, M.Koch and J.Bordas. The program was transferred to Daresbury in the mid 80's where it was restructured and enhanced by J.Bordas and G.Mant. The program is now available for all major hardware platforms (Sun, HP, DEC, SG, PC Linux) in two varieties otoko and xotoko. The former runs on character based terminals and the latter on X windows based workstations. A PC based version is also available from M.Koch (Hamburg). This manual is based on contributions from the original authors and R.Rule (ICI, Runcorn).
The interface is based upon a set of 3 letter instructions, that are preceded with either a dot (e.g. .MUC to multiply a spectrum by a constant) or an asterisk (e.g. *plo to plot a file with x-axis data). The asterisk denotes that instruction requires a set of x-axis data. Most input is then taken from the keyboard, although some functions require the selection of coordinates using either the keyboard cursors or the mouse. OTOKO prompts for filenames with the question:
Enter filename (X99999.XXX[/]) or <ctrl-D>
By entering either <ctrl-d>, ^d or ^D will terminate the prompt without any file input. Nearly all OTOKO functions can be applied to either:
a) a single frame file or a single frame from multi-frame file.
Enter filename (X99999.XXX[/]) or <ctrl-D>: s58026.tmp
In this case only time frame 26 in the file S58001.TMP will be processed.
b) several time frames from one file
Enter filename (X99999.XXX[/]) or <ctrl-D>: s58000.tmp
Enter [1] positional [2] calibrational data or aux[3] [1]: 1
Total number of frames 256
Enter first and last frame, increment or <ctrl-D>: 26,38,2
Memory 1 first and last frame 26 3 incr 2
Enter first and last channel of output [1,256]: <return>
In this case all channels of frames 26,28,30,32,34,36 and 38 of the binary file S58001.TMP will be processed. Another way of obtaining the same result is by giving the name of the first frame followed by a slash (/).
Enter filename (X99999.XXX[/]) or <ctrl-D>: s58026.tmp/
Enter last file number, increment or <ctrl-D>: 58036,2
Enter first and last channel of output [1,256]: <return>
NOTE that the only way to access the contents of binary files other than the SAXS files, is to enter the header file name (e.g. S58000.TMP) and answer the first question with the required choice of file. If a frame number (the last three digits) is non-zero (e.g. S58002.TMP) then the SAXS binary file is always assumed.
c) one time frame from several files in a sequence
Enter filename (X99999.XXX[/]) or <ctrl-D>: s58000.tmp/
Enter last file number, increment or <ctrl-D>: 59000,1000
Enter memory [1]: <return>
Total number of frames: 256
Enter first and last frame, increment or <ctrl-D>: 25
Memory 1 first and last frame 25 25 incr 1
Enter first and last channel of output [1,256]: <return>
In this case all channels of frame 25 of file S58001.TMP and of file S59001.TMP will be processed.
When a command has been executed on a given data file, the output filename is usually given the same extension as the command itself; i.e. after a .DIN command, the output file is Xnn000.DIN.
A full list of commands and a brief description of their operation is provided for the present version:
.ABS Calculate the absolute value of all data points.
.ADC Add a constant to a selected range in spectrum.
.ADD Perform weighted addition of two spectra.
.ADN Add and normalise data in a region of interest.
.ASF Add single file to multiple frames.
.AVE Calculate the average of a multiple set of data files.
.BAK Perform automatic background removal by spline.
.BPK Subtract background under a peak by polynomial fitting.
.CHG Modify selected channels of a spectrum.
.COS Calculate the cosine of data points.
.CPK Determine the major peak parameters.
.CUM Calculate the cumulative sum for a region of interest.
.CUT Cut a frame into a series of frames.
.DER Calculate the first derivative of all data points.
.DIC Divide a constant into a selected range in spectrum.
.DIN Divide and normalise data in a region of interest.
.DIV Perform weighted division of two spectra.
.EXP Calculate the exponential of all data values.
.FCH Calculate the fractional change.
*FFT Compute an in-place DFT using Sande algorithm.
.FIT Perform interactive background fitting.
.FPK Pack a series of frames using frame increment supplied.
*FPK Average a range of frames to a given packing sequence.
.FUN Generate a function.
.GEN Generate a frame of data.
.GIN Generate interpolated x-axis
*GUI Calculate Guinier functions.
*IFT Compute the reverse in-place DFT using Sande algorithm.
*ILT Calculate inverse lattice transform.
.INT Integrate a series of data files.
.ISQ Integrate sequentially using specified sequence.
*ISQ Integrate sequentially using specified sequence.
.ITP Interpolate a series of data points.
.JOI Calculate electron densities from amplitudes.
.LOG Calculate 1000*log (base10) of data.
.LSQ Calculate the least squares fit to a straight line.
.MAX Calculate maximum value of spectrum.
*MAX Calculate max value and position in terms of X data.
.MIR Make a mirror image of spectrum.
.MPL Make a multiple plot of spectra.
*MPL Make a multiple plot of spectra with an x-axis
.MRG Merge a series of frames into one frame.
*MRG Merge a series of frames into one frame with an X-axis.
.MUC Multiply a selected range in spectrum by a constant.
.MUL Perform weighted multiplication of two spectra.
.MUN Multiply and normalise data in a region of interest.
.NBK Background subtraction using variable degree polynomial
.PAK Compress a frame of data by averaging.
.PCC Plot the percentage change.
.PKK Calculate the parameters which describe a peak.
*PLC Produce a correlation plot for a series of frames.
.PLO Plot a series of frames.
*PLO Plot a series of frames with an x-axis.
.PL3 Make a 3D plot of a series of frames.
.PNT Select points and store in file
*POE
.POL Calculate a polynomial of degree M.
*POL Calculate a polynomial of degree M, with an x-axis.
.POW Raise data values to specified power.
.PRO Process raw data up to and including shift.
.PRT Print values of data on laser printer or terminal.
.RBK Background subtraction using straight line fitting
*RMZ Remove zero values from data
.SBK Background subtraction (linear, with same value repeat)
.SEL Select a section of data.
.SEP Separate odd/even values into 2 files
*SFT Compute the Singleton Fast Forward Fourier transform.
.SHO Shift to optimise overlap.
.SIN Calculate the sine of all data points.
.SIT Compute the reverse Singleton Fourier transform.
.SMO Smooth a spectrum using a five point parabola.
.SPL Calculate spline function through data.
*SPL Calculate spline function through data with an X-axis.
.SUM Calculate the sum of a multiple set of data files.
.SUN Subtract and normalise data in a region of interest.
.WIN Create a TUKEY window function for a FFT.
.XAX Generate an x-axis.
.XSH Shift a spectrum in y direction.
.ZER Replace all negative values by zero.
A set of standard files consists of:
Data from the NCD experimental stations appear with filenames of the type
where the first letter refers to the experimental session and the next two digits to the number of the individual experiment. The number increases by one after each experiment until the 100th experiment after which the number returns to zero. This Xnn format can be used to identify any experiment in a session.
The next three digits refer to the type of information contained in the file. The 000 file is the header file and is in ASCII or readable form. It contains information such as the sample title, the number of frames in the file, the names of the intensity and calibration data files. The 001 file contains the raw SAXS data in binary (unreadable) format. The 002 file contains calibration information, again in binary format and finally, the 003 file contains the raw WAXS data also in binary format.
The mdd gives the date on which the data was recorded. The first digit being the duodecimal month and the other digits the date:
The name of a header file is of the form Xnn000.XXX where X is any alphanumeric character and n is any digit. e.g. S74000.TMP. This header file is always written in ASCII and contains the following information:
line 1. Header with up to 80 alphanumeric characters.
line 2. Header with up to 80 alphanumeric characters.
line 3. Integer indicators for the first binary fileindicator(1) = number of channels in each frame.
indicator(2) = number of frames
indicator(3) = 1 (for all 1-D datasets)
indicator(4) = reserved for future use
indicator(5) = reserved for future use
indicator(6) = reserved for future use
indicator(7) = reserved for future use
indicator(8) = reserved for future use
indicator(9) = reserved for future use
indicator(10) = 1, except for the last binary file, when it is zeroline 4. File name of the binary file
The lines 3 and 4 should be repeated for subsequent binary files. The panel below shows an example of a header file with two binary files.
SRS Data recorded on Wed Mar 8 23:54:33 1995
Collagen
512 1 1 0 0 0 0 0 0 1
C01001.308
1 4 1 0 0 0 0 0 0 0
C01002.308
The binary files contain the data, in Fortran terms, as direct access, unformatted, fixed length records (frames) containing REAL*4 values and as a stream of 4 byte floats in "C" terminology. The floating point format, as recorded by the Daresbury data acquisition system, is IEEE format based on "big endian" machines. The contents of these files are organised as indicated by the header file.
The absolute value of all channels.
Enter instruction: .ABS
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.ABS
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Add a constant to a selected range in a spectrum. F(i) = f(i)+c
Enter instruction: .ADC
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.SP1
Enter first and last channel of output [1, 256]: 1, 200
Zero output outside range [Y/N] [Y]: N
Do you want same constant for all spectra? [Y/N] [Y]: <return>
Enter constant [1.0]: 125.0
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.ADC
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Weighted addition of two spectra channel per channel (vector sum). F(i) = w1*f1(i)+w2*f2(i)
Enter instruction: .ADD
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04002.SP1
Do you want same constant for all spectra? [Y/N] [Y]: <return>
Enter weights of first and second spectrum [1.0,1.0]: 4,6
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.ADD
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
A constant given in the ith channel of the calibration file is added to all channels of the ith frame in the input file.
Enter instruction: .ADN
Calibration File
Enter filename (X99999.xxx[/]) or <ctrl-D>: C01002.CAL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01000.SP1
Enter first and last channel of output [1, 256]: 1, 200
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.ADN
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Average of series of spectra.
Enter instruction: .AVE
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.AVE
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Fit a linear background defined by two points, one on either side of a peak, input with the cursor. Can be used for several peaks in a spectrum.
Enter instruction: .BPK
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04003.SP1
Enter first and last channel of output [1, 256]: 1, 200
Plots on log scale but integral linear [N]: <return>
At this point a plot of the spectrum appears on the screen. Use the mouse to indicate the points through which the background curve must pass. Move the cursor to the desired position and press the left button. A cross is drawn at the selected point. Terminate the input by pressing the left button (or middle and left button if the mouse has three buttons). Further questions will appear on the screen.
Enter output filename (Xnn000.xxx): D04000.BPK
Enter first header: Title
Enter second header: Comment
Peak Integrals:
Enter output filename (Xnn000.xxx): D04000.INT
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Modify selected channels of a spectrum.
Enter instruction: .CHG
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Editing file D04005.SP1
Enter channel, new value or <ctrl-D>: 4,4.
Enter channel, new value or <ctrl-D>: 8,8.
Enter channel, new value or <ctrl-D>: <ctrl-D>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
The cosine value of all channels.
Enter instruction: .COS
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.COS
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Determines the major peak parameters, integral, width, position etc. The input will usually be a series of peak data as created by the command .PKK. The output is a file with 12 frames, each frame containing one parameter for the series of input peaks.
Frame Definition, output file generated by .CPK.
frame 1 integral
frame 2 standard deviation (related to width
frame 3 maximum height of peak
frame 4 integer channel number, maximum height
frame 5 mean (ie. position of peak)
frame 6 integer channel number, median
frame 7 integer channel number, mode
frame 8 integer, FWHM
frame 9 Skewness 1
frame 10 Skewness 2
frame 11 integer channel number, first channel of peak
frame 12 integer channel number, last channel of peak
Enter instruction: .CPK
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.PKK
Enter output filename (Xnn000.xxx): D04000.CPK
Enter first and last channel of range: 60,70
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Cumulative value : channel i contains the sum of the first i channels of the input spectrum.
Enter instruction: .CUM
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: 1, 200
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.CUM
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Cuts a frame into a series of frames such that the number of channels in all output frames corresponds to the maximum number of channels requested. All channels between the requested number and the maximum number are set to zero.
Enter instruction: .CUT
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter output filename (Xnn000.xxx): D04000.CUT
Enter channels to be cut (max.10): 1,257,513
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Derivative of a spectrum. F(i)=(f(i+1)-f(i))/(n(i+1)-n(i))
Enter instruction: .DER
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.DER
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Division of a spectrum by a constant. The result of a division by zero is set equal to zero.
Enter instruction: .DIC
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: 1, 200
Zero output outside range [Y/N] [Y]: N
Do you want same constant for all spectra? [Y/N] [Y]: <return>
Enter constant [1.0]: 125.0
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.DIC
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
All channels in the ith frame of the input sequence are divided by the value of the constant in the ith channel of the calibration file.
Enter instruction: .DIN
Calibration File
Enter filename (X99999.xxx[/]) or <ctrl-D>: C03001.CAL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01000.SP1
Enter first and last channel of output [1, 256]: 1, 200
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.DIN
Enter first header: Title
Enter second header: Comment
Calibration file
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Division of two spectra channel by channel. Output(i)=input1(i)/input2(i) The result of a division by zero is set equal to zero.
Enter instruction: .DIV
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter filename [X99999.xxx] or <ctrl-D>: D00101.SP1
Do you want same constant for all spectra? [Y/N] [Y]: <return>
Enter weights of first and second spectrum [1,1: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.DIV
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculates forward Fourier transform using the Sande algorithm and Markel pruning modification.
Enter instruction: *FFT
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04006.SP1
Enter first and last channel of output [1, 256]: 1, 200
Modulus output
Enter output filename (Xnn000.xxx): D04000.MOD
Enter first header: Title
Enter second header: Comment
Phase output
Enter output filename (Xnn000.xxx): D04000.PHA
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Fit a polynomial of arbitary degree to a set of points input from a curve drawn on the screen. This instruction is useful for background subtraction operations.
Enter instruction: .FIT
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: 1, 200
At this point a plot of the spectrum appears on the screen. Use the mouse to indicate the points through which the curve will be fitted. Move the cursor to the desired position and press the left button. A cross is drawn at the selected point. Terminate the input by pressing the left button (or middle and left button if the mouse has three buttons). Further questions will appear on the screen.
Do you want to interpolate and save data? [Y/N] [Y]: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.FIT
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Averages ranges of frames according to a given packing sequence contained in a file generated by the .ASC instruction. A range consists of first frame and last frame. Negative frame numbers are not packed.
Enter instruction: *FPK
Packing sequence
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter output filename (Xnn000.xxx): D04000.FPK
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Averages ranges of frames according to a given packing sequence contained in a file generated by the .ASC instruction. A range consists of first frame and last frame. Negative frame numbers are not packed.
Enter instruction: *FPK
Packing sequence
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter output filename (Xnn000.xxx): D04000.FPK
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculate trigonometric functions, Bessel functions or exponentials over a specified range of the argument.
Enter instruction: .FUN
Enter first and last channel of output [1, 256]: 1, 512
Enter type of function
1:Trigonometric
2:Bessel
3:Exponential
4:Gaussian..[1]: <return>
Enter function
1:SIN(X)
2:COS(X)
3:SIN(X)/X [1]: <return>
Enter value of X in first and last channel or
SMIN SMAX and R for X=2*PI*S*R [0.,10.,1]: <return>
Enter amplitude [1.]: <return>
Display plot [Y/N] [Y]: <return>
Enter output filename (Xnn000.xxx): D04000.FUN
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculate radii of gyration, radii of gyration of cross section, radii of gyration of thickness and extrapolated forward scattering. When more than one frame is input, the output file contains
Frame 1 = radius of gyration
Frame 2 = forward scatter
On the first frame, a plot of the selected region with the result of the fit appears on the screen.
Enter instruction: *GUI
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04006.SP1
Enter first and last channel of output [1, 4]: <return>
Enter option
[1] Radius of gyration
[2] Radius of gyration of cross section
[3] Radius of gyration of thickness [1]: 2
SMIN, SMAX, R, I(0): 1. 625 0.12 264
Enter output filename (Xnn000.xxx): D04000.GUI
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculates inverse Fourier transforms.
Enter instruction: *IFT
X-Axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SPX
Modulus data
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.MOD
Phase data
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.PHA
Enter first and last channel of output [1, 256]: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.IFT
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Sum of the contents of a selected number of channels.
Enter instruction: .INT
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Integral value is: 21215.
Enter first and last channel of output [1, 256]: 1,10
Integral value is: 252.
Enter first and last channel of output [1, 256]: <ctrl-D>
Or if there is more than one file or frame
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.SP1/
Enter last file number, increment or <ctrl-D>: 4127,2
Enter first and last channel of output [1, 256]: <return>
Enter output filename (Xnn000.xxx): D01000.INT
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <return>
Integrate sequentially. The integration limits and channel increment are entered on the terminal. The output is the integral or the integral divided by the channel increment in each range.
Enter instruction: .ISQ
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.SP1
Enter first, last and channel increment in sequence [1,256,1]: 1,200,10
Enter output filename (Xnn000.xxx): D04000.ISQ
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Integrate sequentially. The integration limits are given in a file. The output is the integral or the integral divided by the number of channels in each range. The integration sequence should contain the first and last channel of each integration range.
Enter instruction: *ISQ
Integration sequence
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01001.LIM
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.SP1
Enter output filename (Xnn000.xxx): D04000.ISQ
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Interpolate spectrum into specified nos. of data points.
Enter instruction: .ITP
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.SP1
How many points [512]: 256
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.ITP
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Combine a series of files or frames into a single file.
Enter instruction: .JOI
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter output filename (Xnn000.xxx): D04000.ALL
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculate log(base10) of data for all channels. Values less than 1.0E-20 are set to 1.0E-20 such that the resultant log value is -20.
Enter instruction: .LOG
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.LOG
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Weighted linear least squares fit to a straight line
Enter instruction: .LSQ
X Data
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01001.XAX
Y Data
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.SP1
Enter weighting mode:
[+1] Instrumental 1/SIGMA**2
[0] No weighting
[-1] Statistical 1/Y [0]: 1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.LSQ
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Maximum and Minimum value of spectrum.
Enter instruction: .MAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Maximum value: 655.58 at channel: 67
Minimum value: 0. at channel: 1
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Maximum and Minimum value of spectrum.
Enter instruction: .MAX
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Maximum value: 655.58 at channel: 67 X = 0.235
Minimum value: 0. at channel: 1 X = 0.055
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Mirror image of spectrum i.e. right hand side becomes left hand side.
Enter instruction: .MIR
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.MIR
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Plots a series of frames above each other without overlap.
Enter instruction: .MPL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D58002.SP1/
Enter last file number, increment or <ctrl-D>: 58036,2
Enter first and last channel of output [1, 256]: <return>
Min=0.00 Max=4096.0 Greatest overlap=409.6
Enter new values or <ctrl-D>: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Plots a series of frames above each other without overlap.
Enter instruction: *MPL
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.DAT/
Enter last file number, increment or <return>: 3003,1
Enter first and last channel of output [1, 256]: <return>
Min=0.00 Max=254.0 Greatest overlap=0.00
Enter new values or <ctrl-D>: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Merges spectra to give a single frame output file.
Enter instruction: .MRG
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.SP1
Enter first and last channel of output [1, 256]: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.MRG
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Merges spectra to give a single frame output file.
Enter instruction: *MRG
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.SP1
Enter first and last channel of output [1, 256]: <return>
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D05008.SP1
Enter first and last channel of output [1, 256]: <return>
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: <return>
Do you want to sort the output [Y/N] [Y]: <return>
Do you want to display plot? [Y/N] [N]: <return>
X-axis
Enter output filename (Xnn000.xxx): D03000.XAX
Enter first header: Title
Enter second header: Comment
Enter output filename (Xnn000.xxx): D04000.MRG
Enter first header: Title
Enter second header: Comment
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Multiplication of a spectrum by a constant.
Enter instruction: .MUC
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Zero output outside range [Y/N] [Y]: <return>
Do you want same constant for all spectra? [Y/N] [Y]: <return>
Enter constant [1.0]: 125
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.MUC
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Multiplication of two spectra channel per channel (scalar product).
Enter instruction: .MUL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04002.SP1
Do you want same constant for all spectra? [Y/N] [Y]: <return>
Enter weights of first and second spectrum [1, 1]: 10,12
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.MUL
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
All channels in the ith frame of the input file are multiplied by the value of the constant in the ith channel of the calibration file.
Enter instruction: .MUN
Calibration File
Enter filename (X99999.xxx[/]) or <ctrl-D>: C03001.CAL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01000.SP1
Enter first and last channel of output [1, 256]: 1,200
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.MUN
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Packing of a file. Each channel of the output file contains the average value of a selected number of channels in the input file.
Enter instruction: .PAK
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.SP1
Enter number of channels to be packed [1]: 20
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.PAK
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Percent change. Output(i)=100.*(input2(i)-input1(i))/input(i)
Enter instruction: .PCC
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.PCC
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Subtracts the background under a peak by polynomial fitting to two ranges of points on either side of the peak. Note that the peak must lie in the range LMAX-HMIN
Enter instruction: .PKK
Enter filename (X99999.xxx[/]) or <ctrl-D>: C27002.SP1
Enter degree of polynomial [1]: <return>
Enter range of points on either side of peak
(LMIN,LMAX,HMIN,HMAX): 1,5,60,70
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.PKK
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Plots a three dimensional representation with hidden lines suppressed of a series of frames.
Enter instruction: .PL3
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04000.SP1/
Total number of frames: 256
Enter first and last frame, increment or <ctrl-D>: 1,256,2
Memory 1 first and last frame 1 256 incr 2
Enter first and last channel of output [1, 256]: <return>
Origin on RHS (0) or LHS(1) of screen [0]: <return>
Linear [0] or log [1] plot [0]: <return>
minimum value 1.0000 maximum value 254
Enter new values or <ctrl-D>: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Correlation or Parametric plot. Plots pairs of X-Y values without ordering on X-values for multi-valued functions eg. hysteresis loops. Press <return> between plots.
Enter instruction: *PLC
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter memory for errors, 0 for none [0]: <return>
Enter first and last channel of output [1, 256]: <return>
Enter type of plot (dots (1), full (2), symbol (3), histog (4)
full+symbol (5)) [2]: <return>
Enter option
1:X,Y
2:X,LOG(Y)
3:LOG(X),LOG(Y)
4:X**2,LOG(Y)
5:X**2,LOG(XY)
6:X**2,LOG(X**2.Y)
7:X,LOG(XY)
8:X,LOG(X**2.Y)
9:X,X**2.Y [1]: <return>
Enter plot Title: Plot Title
Enter X-Axis annotation: X-Axis Label
Enter Y-Axis annotation: Y-Axis Label
Automatic scaling [Y/N] [Y]: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Plotter output of a file.
Enter instruction: .PLO
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter memory for errors, 0 for none [0]: <return>
Enter first and last channel of output [1, 256]: <return>
Enter type of plot (dots (1), full (2), symbol (3), histog (4)
full+symbol (5)) [2]: <return>
Enter option
1:X,Y
2:X,LOG(Y)
3:LOG(X),LOG(Y)
4:X**2,LOG(Y)
5:X**2,LOG(XY)
6:X**2,LOG(X**2.Y)
7:X,LOG(XY)
8:X,LOG(X**2.Y)
9:X,X**2.Y [1]: <return>
Enter plot Title: Plot Title
Enter X-Axis annotation: X-Axis Label
Enter Y-Axis annotation: Y-Axis Label
Automatic scaling [Y/N] [Y]: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Plotter output of two files (X and Y). Press <return> between plots. This is useful to plot unequally spaced data points.
Enter instruction: *PLO
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter memory for errors, 0 for none [0]: <return>
Enter first and last channel of output [1, 256]: <return>
Enter type of plot (dots (1), full (2), symbol (3), histog (4)
full+symbol (5)) [2]: <return>
Enter option
1:X,Y
2:X,LOG(Y)
3:LOG(X),LOG(Y)
4:X**2,LOG(Y)
5:X**2,LOG(XY)
6:X**2,LOG(X**2.Y)
7:X,LOG(XY)
8:X,LOG(X**2.Y)
9:X,X**2.Y [1]: <return>
Enter plot Title: Plot Title
Enter X-Axis annotation: X-Axis Label
Enter Y-Axis annotation: Y-Axis Label
Automatic scaling [Y/N] [Y]: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Fit polynomial to data in input spectrum
Enter instruction: .POL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256] : <return>
Enter degree of polynomial [1]: 4
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.POL
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Same as .POL but with X-axis.
Enter instruction: *POL
X-Axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Enter degree of polynomial [1]: 4
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.POL
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
nth power of input spectrum.
Enter instruction: .POW
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter exponent: 2
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.POW
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Lineprinter listing of a file between arbitrary limits. If the print output option is 1 (LP) a file (e.g. PRNAM) is produced. To obtain a hard copy type PRINT PRNAM after exiting OTOKO. During a session all output, including the Comments entered using .COM, is appended to this file.
Enter instruction: .PRT
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Print output [0] TT: or [1] LP: [0]: <return>
Enter first and last channel of output [1, 256]: 1,5
Header file: D04000;1 Frame: 5
First and last channel 1 5
1 1.0000 2 2.0000 3 3.0000 4 4.0000 5 5.0000
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Select and/or shift part of a spectrum.
Enter instruction: .SEL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256] : <return>
Enter number of channels +ve shifts to right, -ve to left: 3
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SEL
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculates forward Singleton Fourier transform.
Enter instruction: *SFT
X-axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04006.SP1
Enter first and last channel of output [1, 256] : 1,200
Modulus output
Enter output filename (Xnn000.xxx): D04000.MOD
Enter first header: Title
Enter second header: Comment
Phase output
Enter output filename (Xnn000.xxx): D04000.PHA
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Shift a spectrum relative to a reference spectrum to optimize overlap. The spectrum to be shifted is expanded by linear interpolation. The best overlap is obtained by minimizing the square of the difference between the spectra in a specified range.
Enter instruction: .SHO
Reference spectrum
Enter filename (X99999.xxx[/]) or <ctrl-D>: X03001.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of overlap range: 20,450
Enter expansion factor for interpolation: 5
Enter number of steps for fine search: 10
Enter [0] for shifted spectrum, [1] for residue output [0]: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SHO
Enter first header: Title
Enter second header: Comment
Reference spectrum
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
The sine value of all channels.
Enter instruction: .SIN
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SIN
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Perform a reverse Singleton Fourier transform.
Enter instruction: .SIT
Modulus data
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.MOD
Phase data
Enter filename (X99999.xxx[/]) or <ctrl-D>: D02001.PHA
Enter first and last channel of output [1, 256]: 1,200
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.MOD
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Each channel in the output file contains the value of the five point parabola through (i-2,i-1,i,i+1,i+2).
Enter instruction: .SMO
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SMO
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Smooths spectra using cubic splines.
Enter instruction: .SPL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first and last channel of output [1, 256]: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): S00000.SPL
Enter first and last channel of output [1, 256]: <return>
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Smooths spectra using cubic splines with the option of creating equally spaced output points.
Enter instruction: .SPL
X-Axis
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04001.XAX
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04002.SP1
Enter first and last channel of output [1, 256]: <return>
Values will be sorted in ascending order of X.
Do you want equally spaced points for output [Y/N] [N]: Y
How many [512]: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SPL
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Calculate the sum of a multiple set of data files for all channels. Data set input sequence is terminated by <ctrl-D>
Enter instruction: .SUM
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04008.SP1
Enter filename (X99999.xxx[/]) or <ctrl-D>: <return>
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SUM
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
The constant in the ith channel of the calibration file is subtracted from all channels of the ith frame of the input file.
Enter instruction: .SUN
Calibration File
Enter filename (X99999.xxx[/]) or <ctrl-D>: C03001.CAL
Enter filename (X99999.xxx[/]) or <ctrl-D>: D01000.SP1
Enter first and last channel of output [1, 256]: 1,200
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.SUN
Enter first header: Title
Enter second header: Comment
Calibration File
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Create a TUKEY window function for FFT's.
Enter instruction: .WIN
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.TMP
Enter first and last channel of output [1, 512]: <return>
Enter start & end of flat top or <ctrl-D> for cursor: 236,276
If you select cursor input a plot of the spectrum appears on the screen. Use the mouse to indicate the start and stop of the flat top by moving the cursor to the desired position and pressing the left button. A cross is drawn at the selected point. Further questions will appear on the screen.
Enter width of side lobe: 10
Do you want to display plot? [Y/N] [N]: <return>
Windowed function
Enter output filename (Xnn000.xxx): D04000.WIN
Enter first header: Title
Enter second header: Comment
Generates a file with equally spaced data points. If the value of the constant is 1, each channel contains the channel number. This instruction is useful for generating X-axis values.
Enter instruction: .XAX
Enter first and last channel of output [1, 256]: <return>
Enter channel and value: 1,1
Enter channel and value: 256,256
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.XAX
Enter first header: Title
Enter second header: Comment
Shift a spectrum along the X-axis
Enter instruction:.XSH
Enter filename (X99999.xxx[/]) or <ctrl-D>: D04005.SP1
Enter first & last channels to shift: 1,200
Enter shift +ve for right -ve for left: -20
Do you want to display plot? [Y/N] [N]: <return>
Enter output filename (Xnn000.xxx): D04000.XSH
Enter first header: Title
Enter second header: Comment
Enter filename (X99999.xxx[/]) or <ctrl-D>: <ctrl-D>
Before accurate structural information can be obtained or comparisons between samples can be drawn, the data must be corrected to produce results in suitable units which contain no experimental artefacts. There are 2 basic steps required to correct the raw experimental data:
Normalisation is performed to compensate for the variation in the intensity of the incident beam flux and takes account of the data collection time and the decay of the synchrotron beam current. This correction (.DIN) is made according to the reading from an ionisation chamber located before or after the sample. If the reading of the ionisation chamber placed after the sample is used, then the normalisation step also accounts for the variation in absorption from sample to sample.
Each element of the detector does not have a uniform response to the incident X-ray photons. This feature may be corrected using a detector response, which is obtained by bathing the detector in uniform radiation from a radioactive source (Fe55). A weighted division (.DIV) of the data by the detector response image removes the fluctuations caused by the non-uniform response. An arbitrary weighting of 1,000,000 : 1 (datafile : det.response image) is always used in order to account for the discrepancy in the relative data collection times; this merely ensures that the experimental intensity units are on a sensible, though arbitrary scale.
The positions of known peaks in the diffraction pattern of wet rat tail collagen are used to calibrate the x-axis of all intensity plots. The corrected collagen datafile will consist of a series of sharp maxima as shown below; this may be confirmed using the .plo command in xotoko.
The order of each peak may be identified according to the relative intensity: the 1st, 3rd, 5th, 9th and 12th orders of wet rat tail collagen are strong. Make a note of the rough channel numbers of two prominent peaks (e.g. 3rd and 12th), then use the .plo command again to establish the exact position by examining these peaks in greater detail. The q-values associated with the peaks may then be determined. In general the q value of the nth order peak is given by: q( nth order) = 2*pi*n / 670
Given the channel numbers and q values of 2 such positions, it is possible generate an x-axis calibration file for the horizontal and vertical directions using the .XAX command in xotoko: It is conventional to use the same output file number for the collagen data file and its associated .xax file. At this stage, all of the necessary data correction parameters for a given station configuration have been determined. These may be used in turn to correct all of the remaining raw data files collected in the same configuration.
To produce one dimensional plots use the *plo command in xotoko. This is similar to the .plo command described earlier but asks for a x-axis calibration file. In order to produce a plot with axes that start at zero it is necessary to disregard the automatic plot scaling and input the required values, using x=0.0 as the minimum x limit. It is often worthwhile performing a rapid .plo just to have a look at the plot and choose suitable scaling limits.
It is possible to produce several graphs on one set of axes by plotting a graph as shown above but entering another filename at the 'Enter filename or <ctrl-D>' prompt instead of pressing <ctrl>D. This produces a problem with scaling, as the scale used on the first set of axes is maintained, meaning that valuable data may be chopped off Plot 1. To alleviate this problem scale the axes manually by replying 'N' to the automatic scaling prompt and inputing a larger range of axes values.
The *plo command can also be used to produce plots with other calibrated x-axes (e.g the change in the integrated scattering per frame as a function of temperature) but an appropriate temperature axis must be set up using the .XAX command in xotoko.
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Soft Condensed Matter - Small Angle Scattering
Macromolecular
Soft Condensed 
Imaging and
Biological
Magnetic
Structures and
Crystallography 
Spectroscopy