rawtiltcoords(1)                                              rawtiltcoords(1)

       rawtiltcoords - Get positions and angles of tomogram points in raw tilt

       rawtiltcoords  options

       Rawtiltcoords produces an IMOD model with points at the coordinates in
       the raw tilt series corresponding to points in a tomogram.  Optionally,
       it can also make a list of the projection angles and the computed defo-
       cus at each point.  Its main use is to allow subvolume averages to be
       computed from raw tilt series images after appropriate modification of
       angles.  The program shares much code and many options with Subto-

       The program allows considerable flexibility as long as several restric-
       tions are followed.  Note that it does not currently operate on any
       image data, but it needs to read file headers.  Each of those required
       files could be replaced with a stub produced by the script Copyheader.
         1) The program must be run from the dataset reconstruction directory.
         2) The raw tilt series stack must still be present or its header must
       be present under the same name.
         3) The tomogram on which points were selected for reconstruction must
       be available and entered with the -volume option, although it need not
       be in the current directory.
         4) The original full reconstruction produced by Tilt, or a copy of
       its header, must be present.
         5) The aligned stack used to generate that reconstruction, or a copy
       of its header, must be present.
         6) The unmodified command file used to generate the reconstruction
       must be supplied.  In other words, either the tilt series alignment,
       tomogram positioning parameters, the X-axis tilt, and the tilt angle
       offset and subarea selections in the Tomogram Generation panel of Etomo
       must not be changed, or else a copy of the correct command file must be
       supplied with the -command option.
         7) If you apply any processing to the volume that was modeled outside
       of Etomo, the header entries for pixel spacing, origin, and tilt angles
       must be preserved in the file entered with the -volume option.  If you
       need to trim some more, use Trimvol; if you need to bin, use Bin-
         8) If you need to apply other software that does not preserve these
       header entries, follow these procedures: Make sure that the file ana-
       lyzed has the same dimensions as the IMOD-based file from which it was
       derived.  Enter the name of the IMOD-based file instead of the analyzed
       file with the -volume option.  Supply a point coordinate file instead
       of a model file for the -center option (use Model2Point(1) with the
       -float option to make such a file).  Other alternatives are to load a
       model onto the IMOD-based file with the -m option and save it again, or
       to run Imodtrans on a model with the -image option and the name of
       the IMOD-based files, and use the resulting model.

       You are free to make an aligned stack from a centered subarea or an
       over-sized area and to change this area between the binned and subvol-
       ume reconstructions.  You can apply any trimming options in the Post-
       processing panel in Etomo.

       See the -AngleOutputFile option in the Tilt man page for the format
       and conventions of the projection angle file.

       Rawtiltcoords 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.

       -root (-ro) OR -RootName       Text string
              Root name of dataset.  For one axis of a dual-axis data set,
              include the "a" or "b" in this name.  This option is required.

       -volume (-v) OR -VolumeModeled      File name
              Name of the volume in which points were selected.  If a model
              file is supplied, this should be the volume that was modeled.
              If a point coordinate file is supplied, the coordinates must
              correspond to pixel positions in this file.  This option is

       -center (-ce) OR -CenterPositionFile     File name
              Name of an IMOD model file or a point coordinate file with the
              desired center positions in the modeled volume.  A point coordi-
              nate file should have one point per line, with its X, Y, and Z
              coordinates separated by spaces, not commas.  These coordinates
              should correspond to pixels in the full file specified with
              -volume, where the first pixel in any dimension spans coordi-
              nates from 0 to 1. This option is required.

       -objects (-ob) OR -ObjectsToUse     List of integer ranges
              If only a subset of objects in the model contain points of
              interest, this option can be used to enter a list of those
              objects (comma-separated ranges are allowed).

       -output (-ou) OR -OutputModel       File name
              Name of output model with positions in raw tilt series.  If this
              option is not entered, the first non-option argument will be
              taken as the output model name.

       -angle (-an) OR -AngleOutputFile    File name
              Name of text file to receive a list of the projection angles at
              each position in the tilt series, as well as defocus values if
              the -defocus option is entered.  This file is produced by
              Tilt; see the corresponding option in that man page for a
              full description of the output.

       -defocus (-d) OR -DefocusFile       File name
              With this entry, the file of project angles specified by -angle
              will also have defocus values for each point.  The entry must be
              one of two forms: either the file name of a file with a list of
              defocus values in nanometers, one per line, underfocus positive;
              or the root name of .com and .log files for a run of Ctfphase-
              flip(1).  In the latter case, typically the entry will just be
              "ctfcorrection", with "a" or "b" added if necessary.  The pro-
              gram will read the .com file to determine the pixel size used
              for CTF correction, and whether tilt angles were inverted; and
              it will read the .log file to find the defocus values for each

       -pixel (-p) OR -PixelSize      Floating point
              The pixel size of the raw stack; this entry is needed only when
              entering a defocus file that is a list of defocus values, and
              only if the pixel size in the aligned stack is not correct.

       -invert (-i) OR -InvertTiltAngles
              Invert tilt angles for defocus computations; this entry is
              needed only when entering a defocus file that is a list of defo-
              cus values.

       -full (-f) OR -FullReconstruction   Text string
              Name of full original reconstruction.  The default is "root-
              name_full.rec", so this entry is needed if that file does not
              exists or if the reconstruction has a different name.  Only the
              header is read from this file.

       -ali (-al) OR -AlignedStack    Text string
              Name of aligned stack file.  The default is "rootname.ali", so
              this entry is needed if that file does not exists or if the
              aligned stack has a different name.  Only the header is read
              from this file.

       -com (-co) OR -CommandFile     File name
              Tilt command file used to make the reconstruction. The default
              is to use "tilt.com", so this option is needed for a dual-axis
              data set or to use a copy of the file.

       -reorient (-re) OR -ReorientionType      Integer
              This option can be used to specify the type of reorientation
              that was applied to the original reconstruction to obtain the
              modeled volume, in the unlikely event that the program cannot
              detect which was used.  Reorientation by rotation around the X
              axis can be detected by the tilt angles in the volume header;
              swapping of Y and Z can be detected only if the "clip: flipyz"
              title is still present.  If necessary, the program will assume
              that swapping occurred if the Y dimension is more than twice the
              Z dimension, or that no reorientation occurred if the Z dimen-
              sion is more than twice the Y dimension.  If the program makes a
              wrong assumption or insists that this option be used, enter a 0
              for no reorientation, 1 for swapping of Y and Z, or -1 for rota-
              tion around X.

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

              Read parameter entries from standard input

       David Mastronarde

       tilt, boxstartend, trimvol, binvol, model2point, imod-

       Email bug reports to mast at colorado dot edu.

IMOD                                 4.9.5                    rawtiltcoords(1)