set vari FILE_ATOM = SAVE_FILE.PDB 
set vari FILE_CTAB = SAVE_FILE.CTAB
set vari FILE_SEQ =   
set vari FILE_SYMM = "?MAIN_SYMM:p21.symm" 
set vari FILE_FOBS = diffract.dat
set vari FILE_CELL = cell.dat 

set vari RESOL_MIN global real = 10.0 
set vari RESOL_MAX global real = 2.5 

set vari MAP_2FOFC global inte = 1 
set vari MAP_FO global inte = 1 
set vari MAP_FOFC global inte = 2 
set vari MAP_WORK global inte = 2 

! normally you do not edit below this line
! ==== end of variables data section  ==================
< ?MAIN_UTILS:get_top_par_19_csd

< 
read file MAIN_UTILS:dummy.dat topo main 
 
set vari MAT_ROT global int = 3 
< load_4mol.com 
read file MAIN_UTILS:seq_sim_penalty.table sequence table 
read file FILE_SEQ sequence protein 

read file FILE_ATOM coor xpl
set vari WORK_SEGM char global segm sele all end 

read file FILE_CTAB ctable
show bonds
if ( IRESULT_0 .le. 0 ) <>utils/calculate.bonds WORK_SEGM

<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

read file FILE_CELL cell
read file FILE_SYMM symm

read file FILE_FOBS refl init limit -999, 0, 0 \ 
     reso RESOL_MIN RESOL_MAX friedel re_read

refl key WORK_REFL sele defined end 
! map section

make map 1 from 0 init -9999 auto_grid cell real
make map 2 from 1 init -9999 
! copy map 2 3
ener all on dens on dens map MAP_2FOFC dens scal 25.

! map calculation from model

< ?MAIN_CMDS:re_phase.cmds WORK_SEGM MAP_WORK
< ?MAIN_CMDS:calc_fofc_diff_map.cmds MAP_2FOFC 2. 1. 
< ?MAIN_CMDS:calc_fofc_diff_map.cmds MAP_FOFC 1. 1.

copy map 2 3


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

ima init cent calc
<SAVE_FILE.VIEW
!<>utils/rama
<>utils/show.cell


ima sele atom name CA C N end col 1 bond

ima from erase
 ima col 245 map 1 dens 0.8 16 16 16 
 ima col  90 map 2 dens 2.0 16 16 16

<?MAIN_CMDS:re_image.cmds WORK_SEGM

return