! MAP_ORIG = is a unit cell map
! MAP_DENS = points to the map which will be skeletonized, by default it
!          is the same as the MAP_ORIG
! CUT_OFF = demarks the density level till which the map will be skeletonized
! SIZE_TOO_SMALL = designates the number of atoms in the connected sekelton
!                fragments below which atoms will be delited
! SIZE_MEDIUM = demarks the border in size between small an large skeleton
!             fragments to enable differentiating created fragments 
!             according to their size by color

set vari MAP_ORIG = MAP_ACT
set vari MAP_DENS = MAP_ORIG
set vari CUT_OFF real = MAP_CONT
set vari SIZE_TOO_SMALL = 10
set vari SIZE_MEDIUM = 100



! normally you do not want to edit lines below

if ( AUTO_SEL .eq. "HISTORY" ) key XX_KEY sele history end
if ( AUTO_SEL .eq. "ACTIVE" ) key XX_KEY sele active end
if ( AUTO_SEL .eq. "WORK" ) key XX_KEY sele  segm name WORK_SEGM end

if ( AUTO_SEL .eq. "WORK" .or. AUTO_SEL .eq. "ACTIVE" ) then
 set vari MAP_DENS = nmaps + 1
 set vari CUSHION = 15
 make map MAP_DENS from MAP_ORIG init 9999 \
      around CUSHION sele XX_KEY end
 make map MAP_DENS from MAP_ORIG copy
end_if

key XX_KEY drop

! ========= END OF HEADER =============
! usually there is no need to edit the lines below 
! -------------------------------------------------------------

set vari MAP_SKEL = nmaps + 1

set vari ITEST int = -1790
! set vari ITEST inte atom sele atom numb $1 end
!	show vari ITEST


delete atom sele segm name #* SKEL end
key old sele all end

make map MAP_SKEL from MAP_DENS init 0 integer
make point init from map MAP_DENS extreme CUT_OFF 100.
make map MAP_SKEL from MAP_DENS local CUT_OFF 100.
make map MAP_SKEL + 1 from MAP_SKEL init 9999 integer copy
make map MAP_SKEL cloud sele all end

make point from map MAP_DENS saddle MAP_SKEL MAP_SKEL + 1 ! test 304 331 

make atom from point ( reindex use_map MAP_SKEL test ITEST ) 

key skeleton sele .not old end
! dele bond sele bond range 10. 1000. end

dele atom sele .not by bond all .and skeleton end
make segm from atom sele skeleton end

! dele bond sele bond range 10. 1000. end
! dele atom sele .not old .a segm range 1 SIZE_TOO_SMALL end

! rena sele skeleton end atom CX
set temp sele skeleton end = 50.
set weigh sele skeleton end = 1.
rename chain X sele skeleton end

! Number of atoms per segment
set col sele skeleton .a segm range 1 SIZE_MEDIUM end col 128
set col sele skeleton .a segm range SIZE_MEDIUM  100000 end col 220

image erase
key image sele .not all end
image sele skeleton .a segm rang 10 100000 end set bond

delete map MAP_SKEL
if ( MAP_DENS .ne. MAP_ORIG ) delete map MAP_DENS
<?MAIN_CMDS:use_atoms.cmds ACTIVE
key active sele skeleton end
return