This input block defines the information for rotation function calculations, including resolution range, integration radius, large-term cutoff, and others.

        Remember that the following general input commands can also be used in this input block - comment, echo, and title.

        This defines the cut-off values for the selection of large-terms. CUT1 is used for selecting large-terms for the RF calculation. CUT2 is used for selecting large-terms for the Patterson correlation coefficient calculation.

        This terminates the input to this block. Unlike the other input blocks, the program will not start the RF calculation.

        This will start the RF calculation with the parameters that have been defined. Additional parameters can still be defined, and the end command is still needed to terminate the input to this block.

        This defines the grid interval that will be used in the RF. Three levels of sampling can be set automatically by the program. The default (NGRDRF=1) uses 3 degree sampling along theta_2, and 2.8125 (360/128) degree sampling along theta_1 and theta_3. For NGRDRF of 2 and 3, the sampling along all three angles will be 3.6 and 5.0 degrees, respectively.

        Coarser sampling of the RF will produce less number of rotation angles to check by the TF. However, a slighter lower RF selection value may need to be used to account for the coarser sampling. Also, rigid-body optimization will be necessary.

        This defines the name of the RF map file, for the input of a RF map.

        This specifies whether a RF map will be read in. RF map files produced from other programs (for example GLRF) can be read in this way.

        This specifies whether the RF values will be output to a map. The name of this file will be automatically assigned by the program, based on the the name of the model PDB file. For example, if your model is in the file coords.pdb, the output RF map file will be called coords_rf.map. Map output has not been implemented yet.

        This specifies how the RF sampling over resolution will be combined. If QMINI is true, the minimum value of the RF will be kept. If it is false, the average of the values will be kept. Note that the sampling over the radius is always combined as the average.

        This specifies whether the structure factors will be normalized for the calculation of the RF. The maximum allowed value for the normalized structure factors is given by EMAX.

        For this normalization, the reflections are first divided into shells. An average intensity is then calculated for each shell, and the normalized intensity is given by the ratio of the reflection intensity over the average intensity.

        This specifies whether the origin of the Patterson map should be removed for the RF calculation.

        This specifies whether the Patterson correlation coefficient will be calculated for the peaks in the RF. This is generally a very slow process, so the default is that the calculation will not be done.

        This specifies the radius of integration for the rotation function. The default is that the program will determine the best radius to use based on the information on the atomic model. In addition, the program can automatically sample additional radii for the RF, given by RADIUS-DRADUS and RADIUS+DRADUS. Therefore, if a non-zero value is given for DRADUS, the resulting RF will be an average of three RF calculations.

        This defines the resolution range for the RF calculation. Two sets of ranges can be specified. If so, the two separate rotation functions will be combined with the minimum or average function. The default resolution range is the same that is given by the resolution command in the Crystal block.

        This defines the angle type to be used for the RF calculation. Default is Eulerian angles.

SAVe-RF-peaks

MSAVRF

[10]

        This defines how many peaks in the RF will be listed in the print file. The program will select the highest peaks in the rotation function.

        This defines the number of shells for dividing the reflection data. This is used for the selection of large terms and for the normalization of reflection intensities.

        This defines how the RF peaks will sorted on output. The default is to sort according to the height in the RF map. If NSRTRF is set to 2, the sorting will be based on the Patterson correlation values.

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