makecomfile(1) General Commands Manual makecomfile(1)
NAME
makecomfile - Create single command file for optional step in tomogram
generation
SYNOPSIS
makecomfile [options] output_file
DESCRIPTION
Makecomfile is used to make a single command file for an optional step
in tomogram generation. Such files are created by Etomo and
Batchruntomo upon need rather than when the data set is set up with
Copytomocoms. The type of command file is determined by the output
filename. For each type of file, the program modifies file names as
appropriate and inserts standard option entries as described below.
These standard entries can be modified and additional entries added
using directives entered with the -change and -one options.
There are two kinds of options: ones that are used by several different
command files (although with slightly different meaning in some cases),
and ones that apply only to a particular command file.
The description of output names set for particular files is in the old
naming style. For image files in the new naming style, the extension
shown will be converted to "_ext.mrc", where "ext" is the extension
shown.
Output File Types
xcorr_pt
File to run Tiltxcorr with patch tracking; requires -root,
-input with "xcorr[ab].com", and -binning with the binning of
the prealigned stack. Inserts PrealignmentTransformFile and
ImagesAreBinned entries and sets output to "setname.fid"; also
initializes OverlapOfPatchesXandY to 0.33,0.33 and Border-
sInXandY to 0.05 times the sizes in X and Y, subject to override
by directives entered in files or with the -one option.
autofidseed
File to run Autofidseed; inserts TrackCommandFile, MinSpacing
of 0.85, and PeakStorageFraction of 1.0.
transferfid
File to run Transferfid; requires -root. Inserts the Corre-
spondingCoordFile entry.
cryoposition
File to run Cryoposition; requires -root and -thickness and
can accept -gpu to control GPU use, -find to specify bead-find-
ing, and -bead with a bead size if it is not available in
track.com.
newst_3dfind
File to run Newstack to make an aligned stack for 3D gold
finding with a different binning from the regular aligned stack;
requires -root, -input with "newst[ab].com", and -binning with
the binning to apply. Sets output to "setname_3dfind.ali".
blend_3dfind
File to run Blendmont to make an aligned stack for 3D gold
finding with a different binning from the regular aligned stack;
requires -root, -input with "blend[ab].com", and -binning with
the binning to apply. Also sets OldEdgeFunctions to 1; sets
output to "setname_3dfind.ali".
tilt_3dfind
File to run Tilt to make a tomogram from 3D gold finding;
requires -root, -input with "tilt[ab].com", and -binning with
the binning of the aligned stack to be used. Also requires
-thickness and can accept -shift to specify a shift in Y and
-use to specify whether to use "setname_3dfind.ali" as the
aligned stack. Sets output to "setname_3dfind.rec".
findbeads3d
File to run Findbeads3d; requires -root and -binning with the
binning of the aligned stack that was used to build the tomo-
gram. Also requires -bead. Sets MinRelativeStrength to 0.05,
MinSpacing to 0.9, StorageThreshold to 0, input to "set-
name_3dfind.rec" and output to "setname_3dfind.mod".
tilt_3dfind_reproject
File to run Tilt to reproject the model from Findbeads3d;
requires -root and -input with "tilt_3dfind[ab].com". Adds Pro-
jectModel entry with "setname_3dfind.mod" and sets output to
"setname_erase.fid".
golderaser
File to run Ccderaser to erase gold beads from the aligned
stack using "setname_erase.fid"; requires -root and -bead, which
is used to set BetterRadius. Sets the output to "set-
name_erase.ali", and sets MergePatches to 1, ExcludeAdjacent to
1, CircleObjects to /, and PolynomialOrder to 0.
sirtsetup
File to run Sirtsetup; sets StartFromZero and set RadiusAnd-
Sigma to 0.4,0.05.
ctf3dsetup
File to run Ctf3dsetup; the required input file is the name
of the reconstruction command file.
restrictalign
File to run Restrictalign; the required input file is the
name of the alignment command file.
reducefiltvol
File to run reducefiltvol; the required input file is the
name of the input image file. A binning entry is required and
may be non-integer. The output image file name will be set to
"setname.red#filt", where "#" is the binning.
OPTIONS
Makecomfile 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 command file to copy commands from or use for program
operations; this entry is not required for all types of files.
Because of this, the input file cannot be entered as a non-
option argument.
-output (-ou) OR -OutputFile File name
Output file for commands, a required entry. The filename deter-
mines the type of output, and must start with one of the names
listed above in Output File Types. If this option is not
entered, the first (not second) non-option argument is taken as
the output file.
-root (-ro) OR -RootNameOfDataFiles Text string
Root name of data files, including axis letter
-style (-sty) OR -NamingStyle Integer
0 if image files have descriptive extensions like ".preali", or
1 or 2 if descriptive text is before the extension ".mrc" or
".hdf". This entry is needed only if the style cannot be deter-
mined from files in the dataset and is needed to produce the
particular command file.
-stackext (-sta) OR -StackExtension Text string
Extension of raw stack excluding the period. This entry is
needed only if this extension cannot be determined from files in
the dataset and is needed to produce the particular command
file.
-single (-si) OR -SingleAxis
This entry can be used to indicate that the dataset is single
axis even though the output com file name ends in "a" or "b".
It is not needed with any of the currently defined output file
types.
-binning (-bi) OR -BinningOfImages Integer
Binning value to place in command file, which is required by
many types of files. For Reducefiltvol, non-integer values are
accepted; otherwise the entry must be an integer.
-bead (-be) OR -BeadSize Floating point
Bead size in pixels, required for findbeads3d.
-use OR -Use3dfindAliInput
Change input file to setname_3dfind.ali if needed for
tilt_3dfind
-shift (-sh) OR -ShiftInY Floating point
Amount to shift reconstruction in Y in tilt_3dfind
-halffloat (-ha) OR -HalfFloatModeOutput Integer
Value of -halffloat option to add to the golderaser command
file: 2 to set the mode for output files to half-floats (16-bit
floats) unconditionally, 1 to do so only when the input file is
floating point, or 0 for regular floating point output. This
option overrides both the "setupset.copyarg.halffloat" and "com-
param.golderaser.ccderaser.HalfFloatModeOutput" directives
entered with -change or -one.
-thickness (-t) OR -ThicknessToMake Integer
Thickness of reconstruction in unbinned pixels for tilt_3dfind
or cryoposition, or thickness of slabs in nanometers for
ctf3dsetup. This entry is required in those cases.
-find (-f) OR -FindBeadsInVolume Integer
Value to set for -find option in cryoposition, should generally
be 0 or 2.
-gpu (-g) OR -UseGPU Integer
Value to set for -gpu option in cryoposition
-procs (-p) OR -NumberOfProcessors Integer
Entry for expected number of CPUs or GPUS for -procs in
ctf3dsetup
-local (-l) OR -LocalAlignValidation Integer
Value for testing local areas to place in command file, which is
an option to Restrictalign
-ratios (-ra) OR -TargetAndMinRatios Two floats
Values for the -target and -minimum options to places in the
Restrictalign command file; use 0 to omit one of the options
-skipbeam (-sk) OR -SkipBeamTiltWithOneRot
Value for the -skipbeam option to place in the Restrictalign
command file.
-change (-c) OR -ChangeParametersFile File name
Name of file with directives for changing parameters. A direc-
tive has the form "comparam.comfile.process.option=value" where
"comparam" is a required prefix for directives to be processed
by Copytomocoms, "comfile" is the root name of the command file
with optional "a" or "b", "process" is the name of a program
being run on a line starting with "$", "option" is an option to
add or modify, and "value" is its value, which may be empty to
remove an option from a command list. Files are processed in
order, and a duplicate entry for an option generally overrides
an earlier one or any changes imposed by this script. However,
for a dual-axis data set, a directive specific to a particular
axis, such as that example, will always be preferred over a
generic directive with no "a" or "b" on the command file name
will. For a single-axis data set, directives with a "b" are
ignored and ones with an "a" or with no "a or "b" are treated
equivalently, such that later ones override earlier ones. (Suc-
cessive entries accumulate)
-one (-on) OR -OneParameterChange Text string
One directive for changing parameters, in the format "com-
param.comfile.process.option=value". Entries with this option
are processed after change files, can override any standard
changes or additions being imposed by the script, and later
entries override earlier ones. (Successive entries accumulate)
-help (-he) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
All files are modified from an input file or made from scratch. An
existing copy of the output file will be made into a backup file by
adding the extension ~.
AUTHOR
David Mastronarde
BUGS
Email bug reports to mast at colorado dot edu
SEE ALSO
copytomocoms
HISTORY
IMOD 5.2.0 makecomfile(1)