#	print "word: $word \n" ; 
	if ( $word !~ m"[a-zA-F]" ) { } #print "word: $word is a number\n" ; }
#	    print "word: $word is a NON-number\n" ; 
#	print "$key: \n" ;
#    print " read para_file: >$file_name<\n" ;
#    print " $nc.) > $line \n" ;
#	print " $key " ;
#	print " :: $value " ;
#	print " \n" ;
#print " read >$file_name< done. \n" ;
#print "read_main_config segm:", @{$whole_file{"SG_LIST"}}, "\n" ;
#    print "WRITE>>>> $file_name topp \n" ;
#    print "write MAIN conf file {", $file_name, ": ", join(" ", @{$save_list{"SG_LIST"}}), "}\n" ;
#	print "WRITE> TEST key $key \n";
#		print "WRITE> TEST scalar $xx {", scalar(@{$save_list{$key}}), " - ", scalar(@{$my_test{$key}}), "} \n";
#		print "WRITE> TEST $xx $key", $m1, " ne ", $m2, "\n";
#    print "WRITE>>>> $file_name NO WRITE \n" ;
#    print "WRITE>>>> $file_name TO WRITE \n" ;
#	print "MY_MAIN $key= TEST LENGHT ", length( @{$save_list{$key}}),"\n"; # , " @{$save_list{$key}} \n\n";
#	print "MY_MAIN $key= @{$save_list{$key}}  \n"; # , " @{$save_list{$key}} \n\n";
		if ( !defined(  ${$save_list{$key}}[0] ) ) { print "$key value = >$val< \n" ; $val = "NONE" ; }
		print LIT "$line\n" ; 
    {	print ">>>>>>>>> $key IS EMPTY \n"; }
     print "crystals: $CRYST \n" ;
     print $my_main{"DFR_FORMAT"}[$CRYST] ;
     print $my_main{"FILE_REFL"}[$CRYST] ;
#     print " MAIN_CONFIG_FILE_TEST> HERE I AM \n" ;
#    print $fh " MAIN_CONFIG_FILE_TEST> HERE I AM \n" ;
	    print "nmb >$nmb<",$my_main{"DFR_LIMIT_H"}[$CRYST], "> <$CRYST>", @{$my_main{"DFR_LIMIT_H"}}, "<\n" ;
#    print "$II >$line<\n" ;
print $fh @lines ;
#    print @u, ' x ', @v, ' x ', @z, "\n";
#    print @u, ' x ', $v, ' x ', @z, "\n";
print "reading PDB file \"$PDB_FILE\" \n" ;
open ( PDB,  "< $PDB_FILE" ) || print "main_config.pm::read_pdb_file> FILE OPEN ERROR: >$PDB_FILE< \n" ;
#	print "[$line]\n" ;
#	print " SUBLINE: { 23456789 23456789 23456789 234567 234567 234567} \n" ;
#	print " SUBLINE: {$sub_line} \n" ;
	    print "UNIT CELL: ", join(" | ", @unit_cell), "\n" ;
#	    print " SUBLINE: {$sub_line} \n" ;
# while ( $words[0] eq " " ) { print "x",  shift (@words) , "\n" ; };
	    print "SPACE GROUP: $group \n" ;
#	    print "[$line]\n" ;
#	    print("---> helix:", $words[4],  $words[5], $words[8], "\n") ;
#	    print " SUBLINE: helix {", $my_pair, "} \n" ;
#	    print "[$line]\n" ;
#	    print( "beta:", $words[5],  $words[6], $words[9]-1, "\n" ) ;
 #    if ( substr($line, 1,4) ne "    " ) { $sub_line = substr( $line, 72,4 ) ; print $sub_line, "\n" ; }
 #	print $nn, " MODEL LINE{", $line, "}", scalar(@words), "-", $seg_name, "-\n" ;
 #	print $nn, " model LINE{", $line, "}", "-", $seg_name, "-\n" ;
  #	if ( $seg_name eq "    " ) { print "TEST SEG NAME {", $seg_name, "}\n" };
  #	if ( $seg_name eq "" ) { print "test SEG NAME {", $seg_name, "}\n" };
#	print "$nres, line_id: <$line_id> \n" ;
  #	    print "{", substr( $line, 16,1 ), "} ", $line; 
#		    print " 1 {", @{$my_mult{$mult_conf}}, "} {", $seg_name, "}\n"; 
  #		    print "{", substr( $atom_name, 0,1 ), "} ", $line; 
#		print " 2 {", @{$my_mult{$mult_conf}}, "} {", $seg_name, "}\n"; 
  #		print " ne H{", substr( $atom_name, 0,1 ), "} \n"; 
#  	print " xyz", @xyz, $xyz[0] + $xyz[1] + $xyz[2], "\n" ;
#	    print "$nres, line_id: <$line_id> >$seg_name< \n" ;
#    print " $nat LAST_LINE_PDB> ", $pdb_records[$#pdb_records], "\n", 	$atom_list[$#atom_list], "\n";
 # print " residues: {", $sub_line, "}\n" ; 
     print " in multiple conf loop: {", $key, " - ", @chras, "}\n" ; 
 	else { 	print " $nmm multiple conf: {", $key, " - ", $chras[$nmm], "}\n" ; }
     print " unstandard multiple conf. $nmm delete: {", $key, "}\n" ; 
#	print " segment names: {", $sub_line, "}\n" ;
#	print " SUBLINE {", $sub_line, "}", scalar(@my_segm_list ), " \n" ; 
     print " multiple conformations : $nmm \n" ; 
#	print " ONE SEGMENT: only \n" ; 
#		print "each subline>$sub_line<\n" ;
#		    print " base $nm >$ch< anepdnix >$cnm<\n" ;
#		print $sub_line, ">". join(" ", @my_segm_list ) , "\n" ;
#	print " ONE SEGMENT: else \n" ; 
#	    print " SUBLINE {", $sub_line, "}", scalar(@my_segm_list ), " \n" ; 
#		print "}", $sub_line, "{ does match: {", $sm, "}\n" ;
#			    print " segment names: {", $ss, "} multi: {", $sm, "}\n" ;
#		print " segment names: {", $sub_line, "}\n" ;
#     print " push 1 on segm list\n";
#    print " my segm list:::", join(" ", @my_segm_list), "\n" ;
    print "main_config::read_pdb> my segm list:::", join(" ", @my_segm_list), "\n" ;
     print "writing PDB file \"$PDB_FILE\" \n" ;
#     print "segm list: ", $x, "\n" ;
     print "resi list: ", $x, "\n" ;
     print "sequ list: ", scalar (@my_sequ_list), "\n" ;
#     print "unit cell: ", join( " ", @my_unit_cell), "\n" ;
#     print "space group: ", @$my_space_group, "\n" ;
#	print $IRS, " iatom:",  $my_sequ_list[$IRS]{"atom_end"}, "\n" ;
#	     print " iatom:", $IATOM,  " - ", $my_sel_list[$IATOM] , "->", $my_sequ_list[$IRS]{"atom_end"},  " :el", $my_atom_el_list[$IATOM], "<",  $#my_atom_el_list, ">", $el_default, "<\n" ;
	     $line = sprintf "ATOM  %5d %5s%4s%1s%5s   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s\n", 
     {     print $pdb_records[$IATOM] ; }
     print PDB @pdb_records ;
# #	print "[$line]\n" ;
# #	print " SUBLINE: { 23456789 23456789 23456789 234567 234567 234567} \n" ;
# #	print " SUBLINE: {$sub_line} \n" ;
# 	print "UNIT CELL:", join("|", @unit_cell), "\n" ;
# #	print " SUBLINE: {$sub_line} \n" ;
# # while ( $words[0] eq " " ) { print "x",  shift (@words) , "\n" ; };
# 	print "SPACE GROUP: $group \n" ;
# #    if ( substr($line, 1,4) ne "    " ) { $sub_line = substr( $line, 72,4 ) ; print $sub_line, "\n" ; }
# #	print $nn, " MODEL LINE{", $line, "}", scalar(@words), "-", $seg_name, "-\n" ;
# #	print $nn, " model LINE{", $line, "}", "-", $seg_name, "-\n" ;
# #	if ( $seg_name eq "    " ) { print "TEST SEG NAME {", $seg_name, "}\n" };
# #	if ( $seg_name eq "" ) { print "test SEG NAME {", $seg_name, "}\n" };
# #	    print "{", substr( $line, 16,1 ), "} ", $line; 
# #		    print "{", substr( $atom_name, 0,1 ), "} ", $line; 
# #		print " ne H{", substr( $atom_name, 0,1 ), "} \n"; 
# #	print " xyz", @xyz, $xyz[0] + $xyz[1] + $xyz[2], "\n" ;
	print "reading TOPOLOGY file \"$FILE\" \n" ;
	open ( TOP,  "< $FILE" ) || print "read_topology_files> FILE OPEN ERROR: >$FILE< \n" ;
#	print $line ;
#		print " residue ", $words[1], "\n" ;
#		print "read_topo> $current\n" ;
	    { print "main_config.pm> read_topo: UNKOWN KEYWORD>> $line<\n" ; }
print "reading MAIN CTAB file \"$MY_FILE\" \n" ;
    open ( PDB,  "< $MY_FILE" ) || print "read_ctab_file> FILE OPEN ERROR: >$MY_FILE< \n"; 
#	    print "$iatom $i [$line] <$leng >\n" ;
#	    print " $iatom |", join( " ", @ct_line), "|\n" ;
    print " fraction{", $fract, "}\n" ;
#	    print " HASH: $select $kind value = {", $value, "}\n" ;
#	    print "segment list ", $word, "\n" ;
#    print "main_config> hydrogen ", $hydrogen_flag, " ",  @{$my_main{"IMAGE_HYDRO"}}, "\n" ;
#print "main_config> ", $chain_memory_flag, " ",  @{$my_main{"IMAGE_CHAIN"}}, "\n" ;
print "creating \"$MACRO_FILE\" \n" ;
#print " image :<", @{$my_main{"IMAGE_MY_FILE"}}, ">\n" ;
#print " image file:<", $my_file, ">\n" ;
    if ( $my_file eq "--NONE--" ) { print " create_re_image> WARNING undefined re_image file $my_file\n" ; }
#    print << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
print MACRO << "END_OF_TEXT" ;
    print MACRO "vlt\n" ;
printf MACRO ( " color 33 red %4.2f green %4.2f blue %4.2f \n",  @{$my_main{"IMAGE_COLOR_1"}} );
printf MACRO ( " color 34 red %4.2f green %4.2f blue %4.2f \n",  @{$my_main{"IMAGE_COLOR_2"}} );
printf MACRO ( " color 35 red %4.2f green %4.2f blue %4.2f \n",  @{$my_main{"IMAGE_COLOR_3"}} );
printf MACRO ( " color 36 red %4.2f green %4.2f blue %4.2f \n",  @{$my_main{"IMAGE_COLOR_4"}} );
printf MACRO ( " color 37 red %4.2f green %4.2f blue %4.2f \n",  @{$my_main{"IMAGE_COLOR_5"}} );
printf MACRO ( " color 38 red %4.2f green %4.2f blue %4.2f \n",  @{$my_main{"IMAGE_COLOR_6"}} );
    print MACRO "exit\n" ;
print "helix:", @hlx, "\n" ;
	    print MACRO " set sec assign sele chain name $sgm end coil\n" ;
	print MACRO " set sec assign sele chain name $sgm .a seq $sq1 : $sq2 end alpha\n" ;
	print MACRO " set sec assign sele chain name $sgm .a seq $sq1 : $sq2 end beta\n" ;
print " chain memory falg: $chain_memory_flag \n" ;
print MACRO << "END_OF_DATA" ;
#    print "sel ID>", $sel_id, "\n" ;
#    print $sel_id, "ssel_id:{", $sel_id, "}\n" ;
    print MACRO 
    print MACRO 
    print MACRO 
    print MACRO "set color \n";
    print MACRO	" sele display end = $ICOLOR\n" ;
    print MACRO "exit\n\n" ;
    print MACRO "set color \n";
    print MACRO
    print MACRO
    print MACRO "exit\n\n" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO 
    print MACRO << "END_OF_TEXT" ;
print MACRO "exit\n\n" ;
    print MACRO 
    print MACRO 
print MACRO "exit\n\n" ;
    print MACRO << "END_OF_TEXT" ;
print MACRO "exit\n\n" ;
    print MACRO "set color \n";
    print MACRO << "END_OF_TEXT" ;
print MACRO "exit\n\n" ;
    print MACRO "set color \n";
{  print MACRO 	" sele display end col 32 \n" ; }
{ print MACRO " sele display end col 0 \n" ; }
{ print MACRO " sele display end col 90 \n" ; }
{ print MACRO " sele display end col 120 \n" ; }
{ print MACRO " sele display end col 140 \n" ; }
{ print MACRO " sele display end col 160 \n" ; }
{ print MACRO " sele display end col 200 \n" ; }
{ print MACRO " sele display end col 220 \n" ; }
{ print MACRO " sele display end col 244 \n" ; }
{ print MACRO " sele display end col 33\n" ; }
{ print MACRO " sele display end col 34 \n" ; }
{ print MACRO " sele display end col 35 \n" ; }
{ print MACRO " sele display end col 36 \n" ; }
{ print MACRO " sele display end col 37 \n" ; }
{ print MACRO " sele display end col 38 \n" ; }
print MACRO "exit\n\n" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
#print " sel id: {", $sel_id, "++", $selections{$sel_id}{"ATOM"}, "}\n" ;
#    print " image radii fraction: $fract \n" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
#print " NONE sel id: {", $sel_id, "++", $selections{$sel_id}{"ATOM"}, "}\n" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
#    print " image radii fraction: $fract \n" ;
    print MACRO << "END_OF_TEXT" ;
    print MACRO << "END_OF_TEXT" ;
#    print " image radii fraction: $fract \n" ;
    print MACRO << "END_OF_TEXT" ;
print MACRO << "END_OF_TEXT" ;
print MACRO << "END_OF_TEXT" ;
#	print " filter list:", $my_file ,"\n" ;
#	    print " filter:", $filter , " - ", $filter_file, "\n" ;
#	    print " my file-> $my_file \n" ;
# #	    print " INSIDE MATHC:", $my_file, "\n" ; 
# #	    print " NO MATHC:", $my_file, " - for - ", $filter_file, "\n" ; 
#    print " main_cof:: make_ctab_link>", $i1, "  ", scalar(@{$i_ctab[$i1]}), "\n" ;
#    print " main_cof:: make_ctab_link>", $i1, "  ", scalar(@{$i_ctab[$i1]}), " $i2\n" ;
    print " read alignment file: >$INPUT_FILE<\n" ;
#if ( $#SEQ_INPUT_LINES <= 0 ) { print " EMPTY FILE: \n" ; exit }
#    print @SEQ_INPUT_LINES, "\n" ;
#	print " seq numb: $#SEQ_INPUT_LINES \n";
	    print $#line_array, " file: >$line<\n" ;
#	print "until  >",  $#line_array, "< $data_flag >\n" ; 
#    print "data: >$line< \n" ;
#	    print " data flag: >", $data_flag, "<\n" ;
	    if ( !exists($seq_data{$id} ) ) { print "push $id\n" ; push(@id_list, $id) ; }
#		print $id, " d: >",$chrs[1],"< \n" ;
#    print " data final flag: >", $data_flag, "-", $line, "<\n" ;
#    print " data final flag: >", $data_flag, "-", $line, "<\n" ;
#    print " data final flag: >", $data_flag, "-", $line, "<\n" ;
#    print " data final flag: >", $data_flag, "-", $line, "<\n" ;
#     print " set matrix 3 number -\n" ;
#     print join( " ", @{$matrix[0]}), " -\n" ;
#     print join( " ", @{$matrix[1]}), " -\n" ;
#     print join( " ", @{$matrix[2]}), "\n" ;
#     print " set vari XTRAN global real = ", $tran3[0], "\n" ;
#     print " set vari YTRAN global real = ", $tran3[1], "\n" ;
#     print " set vari ZTRAN global real = ", $tran3[2], "\n" ;
    print $FH "define init constr inter \n" ;
	print $FH 
    print $FH "\n" ;
#	print " COMPOSIT groups: $IGR, <$GROUP> \n" ;
		print $FH " key outgr  sele .n segm name $LINE end\n" ;
#	print " groups: $IGR, <$GROUP> $MEMBER\n" ;
		    print $FH 
		print $FH 
    print $FH " key outgr drop\n" ;
    print $FH "\n! defining COMPOSIT GROUPS by AUTO method \n" ;
#    print " groups: $IGR, <$GROUP> \n" ;
	    print $FH " define constr occ init\n" ;
	print $FH " define constr occ \(auto \\\n" ;
#	print " member: $MEMBER> ", $NC, scalar(@{$my_main{$GROUP}}), "\n" ;
		print $FH "     sele segm name $MEMBER end \\\n" ;
		print $FH "     sele segm name $MEMBER end \)\n\n" ;
	print $FH "<define_occup_manual.com\n\n" ;