In the description below, each command is shown with the required portion in bold UPPER case. The remaining part of the command can be included for easy readability, but is not required by the program. The names of input variables associated with the command is shown in UPPER case. For character variables, the expected length of the variable is also indiated (for example, ORDOR*5 means ORDOR is a character variable with 5 letters). Variables whose names begin with the letter `Q' are logical variables. A `True' or `False' input is expected for these variables. The 'static' defaults (if any) of the variables are given in square brackets. These default values will generally be used by the program if the command is omitted from input, or if a value of 0 is input to the command. For some variables, the program can provide 'smart' defaults, which depend on the specific calculation being performed. (For example, the integration radius for the rotation function can selected automatically by the program based on the atomic model.) Such variables are indicated with italics.

        This introduces comments in the input file. The entire line will be ignored by the program. An alternative way of introducing comments is with the special character `!'. All characters starting with the ! on the input line are ignored by the program. Comments introduced with the COmment command are echoed at the end of the PRint file, whereas those introduced with the ! character are not.

        This command can be used in the input blocks as well.

        This specifies the level of verbosity of the output to the log file (see PRint command). The default is the most verbose output. Setting the number lower will reduce the verbosity. Error and Warning messages are always output.

        Note that this does not control the output to the PRint file.

        This command can be used in the input blocks as well.

        This command is not implemented as yet.

        This terminates the program calculation.

        This specifies the convention for Eulerian rotation angles. Two conventions are currently supported by the program-

• ZYZ - The first rotation is around the Z axis (q ₃), the second rotation is around the Y axis (q ₂), and the third rotation is around the Z axis again (q ₁). The positive direction of rotation is counter clockwise.


• ZXZ - The first rotation is around the Z axis (q ₃), the second rotation is around the X axis (q ₂), and the third rotation is around the Z axis again (q ₁). The positive direction of rotation is counter clockwise.

        For both conventions, the angles should be input to the program in the following order -- q ₁, q ₂, q ₃, and the program outputs the angles in the same order.

NOTE: The ZYZ and ZXZ conventions are actually equivalent. Therefore, the ZYZ convention should be used for all the calculations, to avoid confusion.

        This terminates the program calculation.

        This specifies the convention for the orthogonalization of the crystal unit cells. The following conventions are currently supported by the program-

• AXABZ - The unit cell a axis is aligned with the Cartesian X axis, and a x b (or the reciprocal cell c* axis) coincides with the Z axis.


• BYBCX - The unit cell b axis is aligned with the Cartesian Y axis, and b x c (or the reciprocal cell a* axis) coincides with the X axis.


• CZBCX - The unit cell c axis is aligned with the Cartesian Z axis, and b x c (or the reciprocal cell a* axis) coincides with the X axis.


• CXCAZ - The unit cell c axis is aligned with the Cartesian X axis, and c x a (or the reciprocal cell b* axis) coincides with the Z axis.


• Y3XYC - This is designed for rhombohedral space groups in the rhombohedral setting only (courtesy of Dr. MRN Murthy). The crystal three-fold axis is aligned with the Cartesian Y axis, and the real space c axis is placed in the XY plane (-X, +Y quadrant).

NOTE: The AXABZ convention is used by the PDB and most other protein crystallography softwares, and therefore should be the only one used in this program as well.

        This specifies the convention for polar rotation angles. Polar angles are defined by three angles, f, y, and k. The angles f and y define a direction in space, which can be considered as a vector starting from the origin of the Cartesian coordinate system. A rotation of k is then applied around this direction, with the counter clockwise rotation being positive.

        Two conventions are currently supported by the program-

• XZK - When the direction vector is projected onto the XY plane of the coordinate system, f is the angle of this projection to the Cartesian X axis (from X going towards +Y being positive). y is the angle between the direction vector and the Z axis.


• XYK - When the direction vector is projected onto the XZ plane of the coordinate system, f is the angle of this projection to the Cartesian X axis (from X going towards -Z being positive). y is the angle between the direction vector and the Y axis.

        For both conventions, the angles should be input to the program in the following order -- f, y, k, and the program outputs the angles in the same order.

NOTE: The XZK convention should be used for most of the calculations. If desired, the XYK convention can be used for monoclinic space groups in the b-unique setting. However, to avoid confusion, it is best to use only the XZK convention, for all calculations.

        This provides a name for the print file of the program. In addition, the program will output summary information (and error messages) to the system output (stdout in Unix jargon), which is terminal screen in interactive mode and job log file in batch mode).

        The output to the print file is not well-organized yet in the current version. The output to the log file is organized better, and should be checked for most purposes. The print file does contain a more complete listing of the MR solutions, whereas the log file only lists the current top 5 solutions.

        This terminates the program calculation.

        This provides a title for the current run of the program. It will be placed at the beginning of each output page. The program will insert the current date and time at the beginning of ATITLE (characters 2-18), and the program will append a version number identifier at the end of ATITLE (characters 111-130).

        This command can be used in the input blocks as well, to modify the title for each component of the calculation.

Go to the previous | next section of the documentation.