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 4.9.10 clonemodel(1)