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 -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. -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 4.11.0 makecomfile(1)