makecomfile(1)              General Commands Manual             makecomfile(1)

       makecomfile - Create single command file for optional step in tomogram

       makecomfile  [options]  output_file

       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

   Output File Types
              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.

              File to run Autofidseed; inserts TrackCommandFile, MinSpacing
              of 0.85, and PeakStorageFraction of 1.0.

              File to run Transferfid; requires -root.  Inserts the Corre-
              spondingCoordFile entry.

              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

              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".

              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".

              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".

              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".

              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

              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.

              File to run Sirtsetup; sets StartFromZero and set RadiusAnd-
              Sigma to 0.4,0.05.

              File to run Ctf3dsetup; the required input file is the name
              of the reconstruction command file.

              File to run Restrictalign; the required input file is the
              name of the alignment command file.

              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
              "", where "#" is the binning.

       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

       -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

       -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

       -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.

       -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

       -procs (-p) OR -NumberOfProcessors       Integer
              Entry for expected number of CPUs or GPUS for -procs in

       -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 (-h) OR -usage
              Print help output

              Read parameter entries from standard input

       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 ~.

       David Mastronarde

       Email bug reports to mast at colorado dot edu


IMOD                                4.12.61                     makecomfile(1)