restrictalign(1) General Commands Manual restrictalign(1)NAMErestrictalign - Restrict tilt alignment parameters for low number of fiducialsSYNOPSISrestrictalign options tiltalign_command_fileDESCRIPTIONRestrictalign will modify the parameter settings in a command file for running Tiltalign so that they are appropriate for the number of fidu- cials available. It does this by applying a series of restrictions - grouping a variable instead of solving at every tilt, or fixing it instead of grouping - in a specified order until an appropriate ratio of measured values to unknown variables is reached. That ratio is picked based on two parameters, the minimum required ratio, and a tar- get ratio. When two restrictions both give more than the minimum ratio, the one closest to the target is chosen. To have the program always pick the first restriction where the ratio is above the minimum, set the target ratio equal to the minimum ratio. The-orderoption controls the order in which restrictions will be applied by changes in the magnification, rotation, and tilt solutions, but these are not the only changes that can occur. Before applying any of these restrictions, the stretching solution (X-stretch and skew), local alignments, and variable X-axis tilt (except between two halves of a tilt series) will be turned off. If these restrictions are suffi- cient, no further changes are made. When there are fewer than 3 beads, the beam tilt solution, projection stretch, and variable X-axis tilt between two halves of a tilt series are turned off; all of these involve solving for a single variable. The solution for one rotation angle is turned off with only one bead. When the ratio of measurements to unknowns falls below the minimum, robust fitting is turned off. The program always changes parameters so as to solve for fewer vari- ables than in the current file. If the ratio is already greater than the minimum and closer to the target than with any restriction applied, no change will be made. To use the program with the default settings with a single-axis tilt series, simply enter: restrictalign align.com The existing file will be renamed to align.com~ and the file with the changed parameters will be written as align.com.OPTIONSRestrictalign uses the PIP package for input (see the manual page for pip). Options can be specified either as command line arguments (with the -) or one per line in a command file (without the -). Options can be abbreviated to unique letters; the currently valid abbreviations for short names are shown in parentheses.-align(-a)OR-AlignCommandFileFilenameCommand file for running Tiltalign. If this option is not entered, the first non-option argument will be used for the name of the command file.-fiducials(-f)OR-NumberOfFiducialsIntegerNumbers of fiducial markers (beads) in the alignment model. With this entry, he program will assume that each bead is marked on every view. If this option is not entered, the program will use the number of contours in the fiducial model with more than one point, and count up the number of points in those contours. The latter will give more accurate estimates of the ratio of measurements to unknowns when there beads marked on only a sub- set of views.-views(-v)OR-NumberOfViewsIntegerNumber of views in the tilt series. If this option is not entered, the program will use the number of views in the image file listed in the command file.-target(-t)OR-TargetMeasurementRatioFloatingpointTarget ratio of measurements to unknown values. If two succes- sive restrictions give a ratio above the minimum required by the-minimumoption, the restriction that gives a ratio closest to this value will be chosen. The default is 3.6.-minimum(-m)OR-MinMeasurementRatioFloatingpointMinimum ratio of measurements to unknown values. Restrictions will be applied until at least one ratio rises above this value. The default is 3.2.-order(-o)OR-OrderOfRestrictionsMultipleintegersOrder in which possible restrictions should be applied to achieve the target. The restrictions are numbered as follows: 1: Group rotations 2: Solve for one rotation 3: Fix tilt angles 4: Group magnifications 5: Fix magnifications The default order is 1,4,3,2,5, which means rotations will be grouped, then tilt angles fixed, then magnifications grouped, then one rotation solved for, then magnifications fixed.-skipbeam(-s)OR-SkipBeamTiltWithOneRotBy default, the program will add a solution for beam tilt if and when it switches to solving for only one rotation angle. (If parameters are already set to solve for only one rotation angle, this switch does not occur and it will not add beam tilt.) With this option, it will not add the beam tilt solution along with this restriction.-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard inputFILESThe input file is renamed by adding a ~ to the end of its name and replaced with the new file.AUTHORDavid MastronardeSEEALSOtiltalignBUGSEmail bug reports to mast at colorado dot edu. IMOD 4.9.10 restrictalign(1)