clonemodel(1)               General Commands Manual              clonemodel(1)



NAME
       clonemodel - clone copies of a model (e.g. an isosurface from a PEET
       average) back to the aligned positions and orientations.

SYNOPSIS
       clonemodel  [options]  -at csv_file  input_model  output_model


DESCRIPTION
       After aligning and averaging a set of subvolumes with PEET and creating
       an isosurface model of the average, it is often useful to create a new
       model containing multple copies of that isosurface reflecting the posi-
       tions and orientations of the individual aligned particles in the orig-
       inal volume. Clonemodel performs this operation. The input_model will
       be cloned at locations and orientations specified in csv_file and the
       output written to output_model. The comma-separated value location/ori-
       entation file, csv_file, will typically have been created by running
       PEET program createAlignedModel(1). The output_model will be silently
       overwritten if it already exists. Neither input_model nor csv_file will
       be modified.

       The PEET alignment and average must have been created with "Align Aver-
       ages Vertically" disabled for proper orientations of the cloned models.

       While clonemodel is designed for use with a csv location file created
       by PEET and a model containing an isosurface rendering of the PEET
       average, this is not required. Except for the first, header line, which
       is always ignored, each line in the location file must contain 7 comma-
       separated fields representing contour number, X, Y, and Z center coor-
       dinates in pixels, and Z-Y-X Slicer angles in degrees (stored in the
       order X, Y, Z), respectively, representing the rotation to be applied
       to the input model.


OPTIONS
       Clonemodel 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.

       -input (-i) OR -InputFile      File name
              Input model file. If this option is not entered, the first non-
              option argument will be used for the input file.

       -output (-o) OR -OutputFile    File name
              Name to give the output file containing cloned copies of the
              input model.  If this option is not entered, the second non-
              option argument will be used.

       -at (-a) OR -AtPoints     File name
              Name of the summary file giving coordinates and orientations at
              which clones are to be inserted.

       -x OR -XRange   Two integers
              The input model will not be cloned at points outside this range.

       -y OR -YRange   Two integers
              The input model will not be cloned at points outside this range.

       -z OR -ZRange   Two integers
              The input model will not be cloned at points outside this range.

       -help (-h) OR -usage
              Print help output.

       -contours (-c) OR -ContourNumbers   List of integer ranges
              A comma and dash separated list of contour numbers. If entered,
              clones will be created only at points belonging to one of the
              specified contours in the model of the original volume.


AUTHOR
       John Heumann  <heumannj at colorado dot edu>

SEE ALSO
       createAlignedModel(1), clonevolume



IMOD                                4.10.10                      clonemodel(1)