xskel

NAME

     xskel- performs skeletonization on an electron density map.

USAGE

     xskel input-file ridgeline-file

DESCRIPTION

     xskel creates ridgeline files by calling mkskel  (mkskel  is
     part of the University of North Carolina GRINCH skeletoniza-
     tion package).  A phase file is used as the input.  The out-
     put  skeletonization  that  was  produced by mkskel from the
     electron density map is renamed as a ridgeline file  with  a
     .bones extension.

     XtalView can read in the ridgeline  file,  or  you  can  use
     grinchbones to convert it to a vu object.

MAIN WINDOW

     Crystal
          The  XtalView  crystal  keyword  accesses  the  crystal
          information file.


     Unit Cell
          This read only field verifies  the  selected  crystal's
          unit cell parameters.


     Directory
          Indicates the current working directory.


     Defaults Menu Button
          A defaults file of parameters can be loaded  and  saved
          in the current directory.


     Input Phase File
          An XtalView phase (.phs) file input.  Electron  density
          will  be  FFT'ed from this phase file and converted for
          input to mkskel. This field can be filled  either  from
          the command line as the first argument, or by selecting
          a file name in the file list, or  by  typing  the  file
          name in.


     Ridgelines File
          The output ridgelines file produced from mkskel  skele-
          tonization.   This  field can be filled either from the
          command line as the second argument, or by selecting  a
          file  name in the file list, or by typing the file name
          in.


     Map Type
          Selects one of the options for map coefficient type.


     Map Bounds in Fractions of the
          Sliders are used to enter the fractional bounds of  the
          volume  to  be skeletonized.  If the bounds are outside
          the slider values, interrupt the program, hand-edit the
          .mi file, then run it through mkskel.


     Resolution
          Optional resolution  filter  to  be  applied  to  input
          phases.


     Minimum density
          Lower this value to see more  ridgeline  contours  than
          the  default  minimum density includes.  Note: XtalView
          maps are always scaled such that 1 rms or sigma  equals
          50.


     Maximum density
          The output ridgelines will be given values from 1 to 29
          corresponding to the min and max entered here.


     Make Ridgelines
          Writes a shell script and starts mkskel  in  the  back-
          ground.


     Cancel
          Stops running mkskel.


     The ridgeline code mkskel was written by Tom  Williams,  and
     is  supplied  with  Xtalview with permission from the author
     and the Computer Science  Department,  University  of  North
     Carolina at Chapel Hill.

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1)