set vari FILE_SEQ = sequence.dat 
! TOPOLOGY AND PARAMETERS SECTION 
topo init 
read param init 
end_of_file

read file >top/top_19_csd.main top main 
read file >top/par_19_csd.main par 
read file >top/top_ion.main top main 
read file >top/par_ion.main par main 
read file >top/top_sme.main top main 
read file >top/par_sme.main par main 
read file >top/top_dna_rna.main top main 
read file >top/par_dna_rna.main par 
set vari DEF_ALL char global = "?MAIN_UTILS:def_top_par_prot_nuc.com" 
set vari FORCE_HBON real global = 30. 
set vari DIST_HBON real global = 1.6 

key background sele .n all end
read file MAIN_UTILS:seq_sim_penalty.table sequence table 
read file FILE_SEQ sequence protein 
! ATOMS SECTION

set vari FILE_ATOM = SAVE_FILE.PDB 
set vari FILE_CTAB = SAVE_FILE.CTAB
set vari FILE_HBOND = SAVE_FILE.HBOND

read file FILE_ATOM atom pdb
set vari WORK_SEGM char global segm sele all end 
set vari II int atom sele segm name WORK_SEGM end
show vari II
if ( II .le. 0 ) then

    set vari WORK_SEGM char global = MOLA 
end_if

 set rad sele segm name WORK_SEGM end vdw

read file FILE_CTAB ctable
show bonds
if ( IRESULT_0 .le. 0 ) then
   <>utils/calculate_bonds_segm.com WORK_SEGM
end_if

read file FILE_HBOND hbond

<DEF_ALL WORK_SEGM
define init group 
! set charge sele .not atom name C CA N H O .a \ 
!    resi name ASP GLU LYS ARG end = 0.0
key active sele segm name WORK_SEGM end
key passive sele segm name WORK_SEGM end

! CRYSTAL FORM 1
set vari FILE_CELL = cell.dat
set vari FILE_SYMM = "?MAIN_SYMM:p1.symm"
set vari FILE_FOBS = diffract.dat
set vari RESOL_MIN global real = 10.0
set vari RESOL_MAX global real = 3.0

read file FILE_CELL cell 
read file FILE_SYMM symm 
read file FILE_FOBS refl init MAIN limit 0 0 0 \
   reso RESOL_MIN RESOL_MAX friedel re_read 

set vari IRESULT_0 global = -1 
refl show key TEST
if ( IRESULT_0 .le. 0 ) then 
refl key TEST sele random 20 1 end 
end_if
refl key TEST sele defined .a TEST end 
refl key WORK_REFL sele defined .a .not TEST end
! map section

make map from 0 empty init auto_grid cell real
set vari MAP_CRYS_1 = nmaps
make map from nmaps empty init 

set vari MAP_2FOFC global inte = MAP_CRYS_1 
set vari MAP_FO global inte = MAP_CRYS_1 
set vari MAP_FOFC global inte = MAP_CRYS_1 + 1 
set vari MAP_WORK global inte = MAP_CRYS_1 + 1 

ener all on dens on dens map MAP_2FOFC dens scal 25.

< SAVE_FILE.MAP

!      final part: opening display, unit cell, chain trace ...

ima cent sele segm numb 1 end
image group on
<SAVE_FILE.VIEW
!<>utils/rama
<>utils/show.cell


image group name CHAIN_TRACE
image sele atom name CA C N .a segm name WORK_SEGM end col 1 bond
ima from erase
 ima col 245 map 1 dens 0.8 26 26 26
 ima col  90 map 2 dens 2.5 26 26 26 
 ener ncs OFF 

<?MAIN_CMDS:re_image.cmds WORK_SEGM

return