mkskel

NAME

     mkskel- performs skeletonization on an electron density  map
     (mkskel  is  part of the University of North Carolina GRINCH
     skeletonization package).

USAGE

     mkskel mainname [-maxlen length -minden density  -range  low
     high]

DESCRIPTION

     mkskel looks for  mainname.mi  (map  information  file)  and
     mainname.map (density map file).  You can create these files
     yourself or use the program xskel to  create  them  for  you
     (see xskel man pages).

     mkskel produces ridgeline files in ascii, binary or "edges",
     depending on the output file format specified.


     Options
          -maxlen takes a specific  length  in  angstroms  as  an
          argument.  This length corresponds to the longest legal
          bond length in the molecule.  The default length is 2.0
          angstroms.

          -minden takes a specific node density in density  units
          as  an  argument.   This  density  corresponds  to  the
          minimum density after range mapping 0-31 that  will  be
          used to make a ridge line.  The default density is 10.0
          density units.

          -range take two arguments:  the highest and lowest den-
          sity  for  the  map  range in density units for mapping
          onto range 0-31 for interp.  The default is  0  density
          units for the low and 99 density units for the high.

     For instructions on writing map information  files  see  the
     README  file in $XTALVIEWHOME/README.mkskel.  mkskel ignores
     file lines that are blank or that start  with  a  "#".   The
     following elements are mandatory:

          1. order - XYZ (or XZY, YXZ, ZYX, ZXY)
               The slowest dimension is  the  first,  the  medium
               dimension  is second, and the fastest dimension is
               third.


          2. dimension - slowsize middlesize fastsize
               slowsize is the size of the data in number of sam-
               pling  points  in  the  slow direction ("number of
               planes").  middlessize is the size in  the  middle
               direction  ("number  of  rows").   fastsize is the
               size in the fast direction ("number of columns").


          3. spacing - slowspace midspace fastspace
               All spacings are in angstroms.


          4. origin - sloworigin middleorigin fast origin

     The following elements are optional:

          1. title - name
               The name of the map.


          2. mapinformat - XXX
               Default mapinformat is character.  Other  possible
               values are:

               ASCII, CHAR, EBCDIC - character format

               FLOAT4, FLOAT - 4-byte floats

               FLOAT8, DOUBLE - 8-byte floats

               INT1, BYTE - 1-byte integer

               INT2 - 2-byte integer

               INT4 - 4-byte integer

          All float and integer values are signed.

          Sample test.mi file

               #################################
               # test.mi

               mapinformat    CHAR
               rloutformat    EDGES

               # name of the molecule
               title          Bovine ferricytochrome b5 fragment
               order          XYZ
               dimension 27 17 17

               #other stuff
               spacing        1.00844 0.959167 0.934687
               origin         -27 -15 -15

               #################################


                    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 Caro-
                    lina at Chapel Hill.

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1), xskel(1)