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.

   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.


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 file to copy commands from; 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 xcorr_pt, autofid-
              seed, transferfid, cryoposition, newst_3dfind, blend_3dfind,
              tilt_3dfind_reproject, tilt_3dfind,  findbeads3d, golderaser, or
              sirtsetup.  If this option is not entered, the first (not sec-
              ond) non-option argument is taken as the output file.

       -root (-r) OR -RootNameOfDataFiles       Text string
              Root name of data files, including axis letter

       -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.

       -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

       -thickness (-t) OR -ThicknessToMake      Integer
              Unbinned thickness of the reconstruction, required for
              tilt_3dfind and cryoposition

       -shift (-sh) OR -ShiftInY      Floating point
              Amount to shift reconstruction in Y in tilt_3dfind

       -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

       -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 (-h) 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                                4.10.10                     makecomfile(1)