rawtiltcoords(1) General Commands Manual rawtiltcoords(1)
NAME
rawtiltcoords - Get positions and angles of tomogram points in raw tilt
series
SYNOPSIS
rawtiltcoords options
DESCRIPTION
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-
mosetup(1).
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-
vol(1).
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.
OPTIONS
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
required.
-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 (-de) OR -DefocusFile File name
With this entry, the file of projection 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
Ctfphaseflip. In the latter case, typically the entry will
just be "ctfcorrection", with "a" or "b" added if necessary.
The program 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 view.
-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" with the old naming style, or "root-
name_full_rec.mrc" with "mrc" naming style, 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" with
old naming style, or "rootname_ali.mrc" with ".mrc" naming
style, 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.
-skip (-s) OR -SkipBackTransform
Skip the back-transformation to the raw stack and output a model
that fits the aligned stack instead.
-distort (-di) OR -ApplyDistortionTransforms Integer
Use this entry to control what the program does when it finds
ambigous information about whether correction for a distortion
field or magnification gradients were done on the aligned stack.
The program looks for this information in both newst.log and
prenewst.log. If it cannot find either log file, it looks in
the respective .com files instead. It considers the situation
ambiguous when only one file is found with distortion correction
options, and refuses to continue unless this option is entered.
Enter 1 to redistort the model when transforming to the raw
stack, or -1 not to.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
AUTHOR
David Mastronarde
SEE ALSO
tilt, boxstartend, trimvol, binvol, model2point, imod-
trans(1)
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 rawtiltcoords(1)