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Optimized for standards. Hosted by Red Hat. If these conditions are not applied, non-zero P r 's can exist at the ends of the real space interval.
If you do not know D max , it is better first not to fix P RMAX , because this value will help to judge whether the chosen interval is correct if, for example, RMAX is too small, P r is systematically higher than zero in the vicinity of RMAX.
Input file parameter INPUT1 is a sequential ASCII file containing the experimental data. The first line is always treated as a problem title comment.
Then the program searches for the first data line. Valid data lines should contain momentum transfer, non-zero intensity, and, optionally, standard deviation in a free format that is, separated by blanks or commas.
After this all valid lines are treated as data; invalid line or end-of-file are considered as the end of the input stream.
The maximum number of data points is This way to read data is rather flexible, allowing to skip additional headers and to use the data with or without the standard deviations.
With modern devices one can measure lots of data points with tiny angular step. This is not always good, and sometimes might become harmful when using indirect methods, because each angular point gives rise to a separate equation, which are, in fact, linearly dependent.
To optimize the performance, GNOM joins neighbouring data points when it finds the number of points to be unreasonably high. The program can handle simultaneously two data sets corresponding to the same sample but recorded with different conditions see below.
The second input file parameter INPUT2 should have the same structure. Default answer to the question ' Input file name, second run ' is no second run.
If some standard deviations or all of them are not specified, negative or equal to zero, the user will be prompted for their estimation parameter DEVIAT.
A positive number means constant relative deviation per point. If the user enters zero default answer , the program will estimate the errors automatically with the help of a polynomial smoothing procedure.
Giving 3 means that for each point with a non-positive standard deviation a relative deviation 0. Some or all of the parameters used by the program can be specified in the configuration file named ' gnom.
The first line of the file is always treated as a comment. The structure of a valid information line is shown below:.
Here NAME is the name of the parameter all names are fixed , the letter in the 9-th column shows the type of the parameter: C - character, I - integer, R - real.
The value of the parameter is to be put between the square brackets not more than 35 characters. If the line is not valid e. When GNOM is started, it first tries to find and read the configuration file in the current directory.
If the local file named ' gnom. If GNOM finds a non-blank value between the square brackets for a parameter in the configuration file, this parameter is assumed to be already defined, therefore, it will not be prompted interactively the other parameters will be asked as usual.
The read-in configuration table is printed on the screen The user can either accept the values or switch to the interactive mode. GNOM assumes the interactive mode also when neither local nor global configuration file has been found.
The example of the global configuration file is shown below. In this file only a few variables are fixed, and the program will not ask for them.
More specific configuration files can be put in the local working directories. They can be configured in such a way, that the program will ask only a few questions or even run in the batch mode.
Examples of the local configuration files can be found in the distribution package. The configuration file may contain arbitrary number of parameters.
Not all of them have to appear in the file: the missing parameters will be treated as non-defined. It is advisable, however, to end the configuration file with the NEXTJOB parameter.
If NEXTJOB is ' Y ' or ' S ', the next lines will describe the parameters for the new job, and so on.
The last line in this case should be:. If you run the NEXTJOB , GNOM keeps the values which were used in the previous job as program defaults for character variables only first 12 characters are kept.
Example: using the general configuration file shown above, the default output file will be ' gnom. The first line of this file should contain three values in free format:.
This should be followed by the form factor values - NFORM of values in 8E To describe the beam divergency in the 2D-case the used should specify the file containing the "spot function", i.
NB and TRANS can be written in the free format separated by blanks or commas NB is compulsory parameter, TRANS - auxiliary.
A comment can be added after TRANS of NBEAM if TRANS is not specified. The beam profile is used to evaluate the smearing due to beam divergency assuming that the curve is obtained by a circular average.
Circularly averaged and normalized profile is used to this end. Additional smearing due to the radial average of the 2D-data is assumed to be one unit in the detector profile.
If instrumental distortions especially all of them are present, the evaluation of the design matrix may become a time-consuming procedure.
When making successive computations with the same experimental conditions and real space limitations, one can use the same integral kernel, if it has been already calculated.
For this, one should answer ' Y ' when prompted ' Is the kernel already evaluated 2549? The program can handle simultaneously two runs recorded at different or the same experimental conditions.
The user should then supply two separate experimental data files first - with lower s range; however, the ranges may overlap and specify explicitly two sets of experimental conditions.
The scale factor for the second run parameter COEF is evaluated by the program automatically . This is a sequential disk file where all the information from GNOM will be printed in ASCII form parameter OUTPUT , default file name is gnom.
Input data for lysozyme is in file lyzexp. It has D max of You may give default answers to other questions. Non-default answers are marked below in italic.
First plot shows how quality estimate varies with different ALPHA : Next there is a reciprocal space fit of scattering computed for final P r function to data: Finally it plots computed distribution function P r :.
Scattering length units s -units used in input file:. Minimum and maximum radii of spheres. Minimum and maximum characteristic particle sizes.
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