! MAP_ORIG = is a unit cell map
! MAP_SKL_DENS = points to the map which will be skeletonized, by default it
!          is the same as the MAP_ORIG
! CUT_OFF = demarks the lower density level till which the map will be skeletonized
! CUT_TOP = demarks the highest 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 CUSHION = SKEL_CUSHION

set vari MAP_ORIG = MAP_ACT
set vari MAP_OLD = nmaps
set vari SIZE_TOO_SMALL = 10
set vari SIZE_MEDIUM = 100
set vari CUT_OFF real = MAP_CONT
set vari CUT_TOP = 15.0

! 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

set vari I_ATOM integer = -1
set vari I_ATOM integer atom sele XX_KEY end

!if ( AUTO_SEL .eq. "WORK" .or. AUTO_SEL .eq. "ACTIVE" ) then
if ( I_ATOM .gt. 0 ) then

 set vari MAP_SKL_DENS = nmaps + 1
 make map MAP_SKL_DENS from MAP_ORIG init 9999 \
      around CUSHION sele XX_KEY end
 make map MAP_SKL_DENS from MAP_ORIG copy
else

 set vari MAP_SKL_DENS = nmaps + 1

 make map MAP_SKL_DENS from MAP_ORIG init 9999 
 make map MAP_SKL_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 = MAP_SKL_DENS + 1
set vari MAP_CLOUD = MAP_SKEL + 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_SKL_DENS init 0 integer
make point init from map MAP_SKL_DENS extreme CUT_OFF CUT_TOP
make map MAP_SKEL from MAP_SKL_DENS local CUT_OFF CUT_TOP
make map MAP_CLOUD from MAP_SKEL init 9999 integer copy
make map MAP_CLOUD cloud

!image col 220 poin dens numb
!return

make point from map MAP_SKL_DENS saddle MAP_CLOUD MAP_SKEL ! test 304 331 
make atom from point ( reindex use_map MAP_CLOUD 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
set col sele skeleton end = 220

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

rena segm SKEL sele skeleton end

! delete map MAP_SKEL
if ( MAP_SKL_DENS .eq. MAP_OLD + 1 ) delete map MAP_SKL_DENS
<?MAIN_CMDS:use_atoms.cmds ACTIVE
key active sele skeleton end
return