Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells MTROTLONG(1) MTROTLONG(1) NAME mtrotlong - extract MTs rotated into longitudinal orientation SYNOPSIS mtrotlong DESCRIPTION Mtrotlong can be used to extract a series of subvolumes with fibrous elements such as microtubules (MTs) rotated into a longitudinal orientation, and with one end of the item in the center of the extracted subvolume. To use it, model each fiber in 3dmod with a single open contour along its axis. Then run Mtrotlong with entries indicating which contours to analyze and how to orient them, and it will produce an IMOD command file for extracting the subvolumes with Rotatevol. This command file would then be run with "subm command_file". This allows the rotation angles to be edited if necessary to produce a better result, using angles found in the Slicer window. The program will determine the orientation near the end of a fiber by fitting to a specified number of points. It is thus desirable to have different fibers modeled with points at roughly equivalent spacings. For example, if some fibers are modeled very densely while others are modeled with only a few points over a long distance, then the fit will be over a very short distance in the former case and over a very long distance in the latter if it is determined from the same number points in each case. The orientation may be less than optimal in both cases. Another way to avoid this problem is to enter different values for the number of points to fit. The program can produce subvolumes with double the sampling in the Z dimension, i.e. half the pixel size. Do do this, it issues commands to extract the volume twice, one with an odd Z size and once with an even Z size, which results in a half-pixel offset. These files are then combined by running Newstack with a file named "interleave", which is also produced by Mtrotlong. The program will extract a volume at either the starting or the ending point of a contour. To have it do both, just make two entries for the contour. Each subvolume will be named with a starting letter that encodes the object number, the contour number, an ending letter that encodes with it is from the start or end of a contour, and the extension .st. Inputs to the program: Name of input model file Name of output command file Name of input image file 1 if the volume has been flipped or rotated so that the X/Y planes are the plane of the sample, or 0 if not (i.e. if it still needs to be loaded into 3dmod with flipping) 1 for an isotropic volume, 2 for a volume with double sampling (half the pixel size) in the Z dimension X, Y and Z size of a single isotropic extracted volume. If the sampling is doubled in Z, the final volume will have Z size 2 * NZ + 1 Single letter codes for each object; for example if object 1 has kinetochore and object 2 has nonkinetochire MTs, the entry could be "kn" Two single letter codes for volumes extracted from contour starts and ends, respectively. A series of lines with the following format: Object number, contour number, 0 or 1 to extract from contour start or end, 0 or 1 to rotate so that the fiber extends upward or downward from the middle, and the number of points to fit over A line with 0,0,0,0,0 to end the series and exit the program HISTORY Written by David Mastronarde about 1996 Incorporated in IMOD 9/11/06