realscalemod(1)             General Commands Manual            realscalemod(1)



NAME
       realscalemod - to scale a model to microns, adjusting for tilts

SYNOPSIS
       realscalemod

DESCRIPTION
       REALSCALEMOD will take a model and rescale it into microns.  It will
       adjust not only for pixel size and section thickness but also for any
       tilts during microscopy.

       If the sections were significantly tilted during microscopy, the pro-
       gram can adjust for these tilts given the proper information.  Prepare
       a file in which the first line shows the Z value and the tilt of the
       first tilted section (or of the first section, if that one was tilted),
       and each successive line shows the Z value and tilt for each section on
       which tilt was changed.  Z values should occur in ascending order.

       Entries to the program are:

       Name of model file to be scaled

       Name of output file in which to place scaled model

       Name of file with tilt information, or Return if none

       IF the model has no scaling information in its header, also make the
       following three entries:

            Magnification of negatives (without any commas)

            Scale, in microns per pixel, at which negatives were digitized

            Section thickness in nanometers

HISTORY
         Written by David Mastronarde, 11/19/93; modified for IMOD 4/24/97

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                 5.2.0                     realscalemod(1)