copytomocoms(1) copytomocoms(1) NAME copytomocoms - Create command files for generating tomograms SYNOPSIS copytomocoms [options] -name rootname DESCRIPTION Copytomocoms generates the command files needed for nearly all of the processing involved in generating a tomogram. The program is run by the setup page of eTomo. There are several ways in which tilt angles can be entered: as a start- ing and increment tilt angle, in a file with a list of angles (which can be extracted from the image file or supplied separately), or directly as a list of angles. For each axis, one of these option must be entered for the tilt angle entry, but only one way can be specified. Options Copytomocoms 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 -): -name OR -RootName File name Root name of data set (omit a or b for dual-axis set) -dual OR -DualAxis Dual-axis data set -montage OR -MontagedImages Data are montaged -backup OR -BackupDirectory File name Directory for backing up small files. Commands to save such files are placed ina script named "savework", which is run at end of every command file. The directory need not exist yet. -pixel OR -PixelSize Floating point Pixel size of images in nanometers. This entry is required. -gold OR -GoldBeadSize Unknown argument type Size of gold beads in nanometers. This entry is required. Enter an arbitrary number like 1 if you are not going to track fiducials. -rotation OR -RotationAngle Floating point Angle from the vertical to the tilt axis in raw images for the A axis or only axis. This entry is required. -brotation OR -BRotationAngle Floating point Angle from the vertical to the tilt axis for B axis. This entry is required for a dual-axis set. -firstinc OR -FirstAndIncAngle Two floats First tilt angle and tilt angle increment for the A axis or only axis. -bfirstinc OR -BFirstAndIncAngle Two floats First tilt angle and tilt angle increment for B axis -userawtlt OR -UseRawtltFile Take tilt angle from a .rawtlt file for the A axis or only axis. -buserawtlt OR -BUseRawtltFile Take tilt angle from a .rawtlt file for B axis -extract OR -ExtractAngles Extract tilt angles from data file for the A axis or only axis. This entry implies -userawtlt. -bextract OR -BExtractAngles Extract tilt angles from data file for B axis -angles OR -TiltAngles List of integer ranges Complete list of tilt angles for the A or only axis, on one line with no spaces. -bangles OR -BTiltAngles List of integer ranges Complete list of tilt angles for the B axis -skip OR -ViewsToSkip List of integer ranges List of views to exclude from processing for A or only axis. This entry and the next are fed into view exclusion lists in track*.com, align*.com, and tilt*.com. -bskip OR -BViewsToSkip List of integer ranges List of views to exclude from processing for B axis -distort OR -DistortionField File name Correct image distortion with the given .idf file. The file will be copied to the current directory. -binning OR -BinningOfImages Integer Binning of the raw images; this entry is needed for distortion correction unless there is no ambiguity about whether they are binned; i.e., unless the images are not binned and are too large to be considered binned. -gradient OR -GradientTable File name Correct for magnification gradients using the given .mgt file. Extractmagrad will be run to extract mag gradient files for each axis. -focus OR -FocusWasAdjusted Focus was adjusted between frames when acquiring montage for the A axis or the only axis -bfocus OR -BFocusWasAdjusted Focus was adjusted between montage frames for the B axis -voltage OR -VoltageInKV Integer Microscope voltage in kV -Cs OR -SphericalAberration Floating point Spherical aberration -ctfnoise OR -NoiseConfigFile File name Configuration file listing noise files for ctfplotter -defocus OR -Defocus Floating point Defocus in nanometers, with underfocus positive -CTFfiles OR -CopyCTFfiles Integer Just copy files for CTF plotting and correction (1 for plotting, 2 for correction, 3 for both) -xsize OR -XImageSize Integer X size of image data (needed if data file not present) -ysize OR -YImageSize Integer Y size of image data (needed if data file not present) -StandardInput Read parameter entries from standard input FILES All files are modified from the master files in the $IMOD_DIR/com directory. Existing copies of the command files will be made into backup files by adding the extension ~. AUTHOR David Mastronarde BUGS Email bug reports to mast at colorado dot edu SEE ALSO extracttilts, extractpieces, extractmagrad HISTORY Copytomocoms was a original a C-shell script. In February 2011 it was converted to Python. BL3DEMC 4.3.7 copytomocoms(1)