branches to the Patterson transform level of DISCUS The Patterson transform is calculated from two input files. The two files must contain the intensity, real or imaginary part, or amplitude in one of the following combinations:
file a file b ------------------------- intensity amplitude real imaginary
The user must specify the Fourier plane that had been calculated and the real space plane to be calculated.
Further help topics are:
Valid commands at this level are:
@ ! execute a macro file (see main help) = ! assigns the value to a variable (see main help) abs ! defines the coordinate of the abszissa echo ! echo a string (see main help) eval ! Evaluates an expression for interactive check (see main help) exit ! terminates Fourier level file ! defines the input file name(s) form ! defines the input file format help ! help to fourier commands (see main help) layer ! defines the layer in reciprocal space to be calculated ll ! defines the lower left corner in reciprocal space lr ! defines the lower right corner in reciprocal space na ! defines the number of points along the abszissa no ! defines the number of points along the ordinate ord ! defines the coordinate of the ordinate rhoabs ! defines the coordinate of the real space abszissa rholayer! defines the layer in real space to be calculated rholl ! defines the lower left corner in real space rholr ! defines the lower right corner in real space rhona ! defines the number of points along the real space abszissa rhono ! defines the number of points along the real space ordinate rhoord ! defines the coordinate of the real space ordinate rhoul ! defines the upper left corner in real space run ! starts the calculation scale ! defines an overall scale factor set ! sets various parameters show ! shows the current settings for the inverse Fourier transform system ! Executes operating system command (see main help) type ! defines the file type (intensity, amplitude ...) ul ! defines the upper left corner in reciprocal space wait ! Waits for user input (see main help)
Defines which the component of the vector parallel to the abszissa is written to the output file.
Defines the filenames needed for the patterson.
The Patterson transform is calculated from one or two input files. The two files must contain the intensity, real or imaginary part, or amplitude in one of the following combinations:
file a file b ------------------------- intensity amplitude real imaginary
If the input format is 'shelxl' then one input file is sufficient. DISCUS assumes the input file to be a SHLEXL List type 5 containing <h> <k> l> <Fobs> <Fcalc> <phase angle in degree> The file is read as free format.
Defines the input format that will be used. Valid parameters are: "gnu" Sets the type of the output file to gnuplot. The intensities are written in blocks of intensities along the abscissa, with an empty line separating each block. Each line of each block contains: index along abscissa, index along ordinate, intensity, third index. "stan" Sets the output to standard file format, which is used by KUPL. The output file contains two initial lines and then a block for each data line separated by an empty line. The first line contains the number of data points along the abszissa and the ordinate, the second line the minimum and maximum value of the indices in reciprocal space along the abscissa and ordinate respectively. "shelxl" Sets the input file format to SHELXL. DISCUS assumes the input file to be a SHLEXL List type 5 containing
<h> <k> l> <Fobs> <Fcalc> <phase angle in degree>
The file is read as free format. All reflections are expanded by the appropriate symmetry operations, including proper phase transformation.
sets the lower left, lower right and upper left corner of the Fourier plane to be calculated and sets the number of data points along the horizontal and the vertical
Sets the lower left corner of the Fourier plane to be calculated.
Sets the lower right corner of the Fourier plane to be calculated.
Sets the number of data points that will be calculated along the abszissa.
Sets the number of data points that will be calculated along the ordinate.
Defines which the component of the vector parallel to the ordinate is written to the output file.
Defines which the component of the vector parallel to the real space abszissa is written to the output file.
sets the lower left, lower right and upper left corner of the real space plane to be calculated and sets the number of data points along the horizontal and the vertical
Sets the lower left corner of the real space plane to be calculated.
Sets the lower right corner of the ral space plane to be calculated.
Sets the number of data points that will be calculated along the real space abszissa.
Sets the number of data points that will be calculated along the real space ordinate.
Defines which the component of the vector parallel to the real space ordinate is written to the output file.
Sets the upper left corner of the real space plane to be calculated.
Starts the inverse Fourier calculation.
Defines an overall scale factor. Together with the automatic scaling by 1/vol(unit cell), this scale factor serves to put the electron density on an absolute scale of electrons per cubic Angstroem. The scale factor should effectively multiply the observed F(000) such that it is equal to F(000) calculated for one unit cell of the average structure.
Every time you enter "patterson" the scale factor is calculated to be number of atoms in crystal / number of atoms in one unit cell. If you use experimental data, you MUST specify the scalefactor everytime you enter the "patterson" submenu.
Set defines various parameters. "accu" Sets the mode for the accumulation of Patterson transforms. "init" The electron density array is initialised, i.e. set to zero. "add" The next Patterson transform is added to the previous value. This way several Patterson transforms will contribute to a single layer in direct space, which is necessary to create a Patterson section rather than a projection onto the layer. See the manual for further details.
shows the current settings for the Fourier transform file
Defines the content of file "a" or "b".
The Patterson transform is calculated from one or two input files. The two files must contain the intensity, real or imaginary part, or amplitude in one of the following combinations:
file a file b ------------------------- intensity amplitude real imaginary
If the input format is "shelxl", DISCUS reads just one file. You can calculate the inverse Fourier from Fobs or Fcalc data by choosing the appropriate file type from one of the following choices:
file a file b ------------------------- amplitude fobs fcalc
Sets the upper left corner of the Fourier plane to be calculated.