xplor 3.8.4.3

Joseph Nachman nachman at hera.med.utoronto.ca
Tue Apr 1 12:54:15 EST 1997


I'm having trpouble with version 3.8.4.3 of X-PLOR: it objects to the
records in the reflection file.

Here is the output file:

---------------------------------------------------------------------


 X-PLOR(online) Version 3.843

 Author: Axel T. Brunger
 X-PLOR(online): Copyright 1996 by Yale University
 X-PLOR: Copyright 1987 by Harvard U., 1988-1996 by Yale U.

 User: nachman      on: PS6000          at: 31-Mar-97 17:30:45
 X-PLOR> remarks  file  xtal_maps/map.inp 
 X-PLOR> remarks  compute electron density maps of the type  ( a Fobs - b Fobs ) 
 X-PLOR> 
 X-PLOR>{===>} structure @yeei_3.psf  end                        { read structure file } 
 ASSFIL: file yeei_3.psf opened.
 STRUcture>PSF 
 REMARKS FILENAME="yeei_3.psf"
 REMARKS  TOPH19.pep -MACRO for protein sequence
 REMARKS DATE:16-Jan-97  17:32:28       created by user: nachman
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       2100(MAXA=       24000)  NBOND=       2140(MAXB=       24000)
 NTHETA=      3068(MAXT=       40000)  NGRP=         210(MAXGRP=     24000)
 NPHI=        1226(MAXP=       50000)  NIMPHI=      1006(MAXIMP=     24000)  
 NDON=         418(MAXPAD=      4000)  NACC=         312(MAXPAD=      4000)
 NNB=            0(MAXNB=       3000) 
 STRUcture>  end                        { read structure file } 
 X-PLOR> 
 X-PLOR>{===>} coor @yeei_b3a.pdb     end 
 ASSFIL: file yeei_b3a.pdb opened.
 COOR>REMARK FILENAME="yeei_b3a.pdb" 
 COOR>REMARK  TOPH19.pep -MACRO for protein sequence 
 COOR>REMARK DATE:26-Feb-97  10:20: 6       created by user: nachman 
 COOR>ATOM      1  CB  ALA     2      -4.358   4.338  -8.476  1.00 33.66      AAAA 
 COOR>ATOM      2  C   ALA     2      -5.767   4.908  -6.503  1.00 33.17      AAAA 
 X-PLOR>     end 
 %X-PLOR-ERR: "END" not allowed. "STOP" terminates program
 X-PLOR>                                                         { read coordinates    } 
 X-PLOR> 
 X-PLOR>{{===>}      @ortho.fix                                  { put coordinates into }} 
 X-PLOR>                                                    { X-PLOR orthogonalization } 
 X-PLOR>                                                                { convention   } 
 X-PLOR> 
 X-PLOR> xrefine 
 XREFINE> 
 XREFINE>{===>} 
 XREFINE> 
 XREFINE> 
 XREFINE>   a=33.023 b=54.102 c=57.530 alpha=90.0 beta=99.60 gamma=90. 
 XREFINE> 
 XREFINE>{===>} 
 XREFINE>   symmetry=(x,y,z)                  {*Symmetry operators for crystal P2(1)   *} 
 XREFINE>   symmetry=(-x,y+1/2,-z) 
 XREFINE> 
 XREFINE>   SCATter ( chemical C* ) 
 SELRPN:   1064 atoms have been selected out of   2100
 SCATTER_A1=      2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 
 XREFINE>   SCATter ( chemical N* ) 
 SELRPN:    300 atoms have been selected out of   2100
 SCATTER_A1=      12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 
 XREFINE>   SCATter ( chemical O* ) 
 SELRPN:    312 atoms have been selected out of   2100
 SCATTER_A1=      3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 
 XREFINE>   SCATter ( chemical S* ) 
 SELRPN:      6 atoms have been selected out of   2100
 SCATTER_A1=      6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 
 XREFINE>   SCATter ( chemical P* ) 
 SELRPN:      0 atoms have been selected out of   2100
 SCATTER_A1=      6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645 1.11490 
 XREFINE>   SCATter ( chemical FE* ) 
 SELRPN:      0 atoms have been selected out of   2100
 SCATTER_A1=      11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566 0.97070 
 XREFINE> 
 XREFINE>{===>} 
 XREFINE>   nreflections=50000 
 XREFIN: allocating space for   50000 reflections.
 XREFINE>   reflection @yeei.xpl      end                            { read reflections } 
 ASSFIL: file yeei.xpl opened.
 REFLection> NREFlections=    19647 
 REFLection> ANOMalous=FALSE 
 REFLection> DECLare NAME=FOBS         DOMAin=RECIprocal   TYPE=COMP END 
 REFLection> DECLare NAME=SIGMA        DOMAin=RECIprocal   TYPE=REAL END 
 REFLection> INDEX=   0   2   3 FOBS=      4.38 SIGMA=      1.38 
 %REFLection-ERR: unrecognized command:
  INDEX=   0   2   3 FOBS=      4.38 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   2   3 FOBS=      4.38 SIGMA=      1.38 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   3   1 FOBS=      3.05 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   3   1 FOBS=      3.05 SIGMA=      0.93 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   3   3 FOBS=     19.01 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   3   3 FOBS=     19.01 SIGMA=      2.11 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   4   1 FOBS=     25.34 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   4   1 FOBS=     25.34 SIGMA=      2.29 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   4   3 FOBS=      9.89 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   4   3 FOBS=      9.89 SIGMA=      1.42 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   1 FOBS=     11.76 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   1 FOBS=     11.76 SIGMA=      0.83 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   3 FOBS=      9.10 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   3 FOBS=      9.10 SIGMA=      1.24 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   5 FOBS=     13.43 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   5 FOBS=     13.43 SIGMA=      1.19 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   7 FOBS=      6.95 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   7 FOBS=      6.95 SIGMA=      2.04 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   8 FOBS=    103.75 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   5   8 FOBS=    103.75 SIGMA=     10.95 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   0 FOBS=     36.97 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   0 FOBS=     36.97 SIGMA=      4.05 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   1 FOBS=     12.63 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   1 FOBS=     12.63 SIGMA=      0.83 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   2 FOBS=     47.62 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   2 FOBS=     47.62 SIGMA=      3.52 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   3 FOBS=      8.57 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   3 FOBS=      8.57 SIGMA=      0.81 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   4 FOBS=     79.34 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   4 FOBS=     79.34 SIGMA=      8.04 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   5 FOBS=      8.44 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   5 FOBS=      8.44 SIGMA=      0.87 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   6 FOBS=     92.02 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   6 FOBS=     92.02 SIGMA=      9.26 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   7 FOBS=     11.85 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   7 FOBS=     11.85 SIGMA=      2.05 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   8 FOBS=     69.23 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   6   8 FOBS=     69.23 SIGMA=      7.97 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   1 FOBS=     14.49 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   1 FOBS=     14.49 SIGMA=      1.01 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   2 FOBS=     14.26 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   2 FOBS=     14.26 SIGMA=      1.17 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   3 FOBS=      6.96 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   3 FOBS=      6.96 SIGMA=      0.95 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   4 FOBS=     32.88 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   4 FOBS=     32.88 SIGMA=      2.18 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   5 FOBS=      2.02 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   5 FOBS=      2.02 SIGMA=      1.46 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   6 FOBS=     78.84 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   6 FOBS=     78.84 SIGMA=      6.15 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   7 FOBS=     11.78 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   7 FOBS=     11.78 SIGMA=      1.63 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   8 FOBS=    116.28 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   8 FOBS=    116.28 SIGMA=     13.49 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   9 FOBS=     10.69 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7   9 FOBS=     10.69 SIGMA=      2.54 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7  12 FOBS=    113.11 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7  12 FOBS=    113.11 SIGMA=     11.80 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7  13 FOBS=     18.42 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7  13 FOBS=     18.42 SIGMA=      3.68 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7  14 FOBS=     22.24 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   7  14 FOBS=     22.24 SIGMA=      3.81 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   1 FOBS=     18.89 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   1 FOBS=     18.89 SIGMA=      1.23 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   2 FOBS=     59.91 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   2 FOBS=     59.91 SIGMA=      3.75 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   3 FOBS=      7.11 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   3 FOBS=      7.11 SIGMA=      1.10 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   4 FOBS=    100.92 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   4 FOBS=    100.92 SIGMA=      7.32 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   5 FOBS=      4.15 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   5 FOBS=      4.15 SIGMA=      1.25 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   6 FOBS=    119.12 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   6 FOBS=    119.12 SIGMA=     12.43 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   7 FOBS=     20.38 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   7 FOBS=     20.38 SIGMA=      2.50 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   8 FOBS=    202.38 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   8 FOBS=    202.38 SIGMA=     20.71 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   9 FOBS=     10.63 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8   9 FOBS=     10.63 SIGMA=      1.99 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  10 FOBS=    117.24 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  10 FOBS=    117.24 SIGMA=     13.30 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  12 FOBS=    115.82 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  12 FOBS=    115.82 SIGMA=     12.50 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  13 FOBS=     12.10 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  13 FOBS=     12.10 SIGMA=      4.05 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  15 FOBS=      8.05 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  15 FOBS=      8.05 SIGMA=      8.56 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  16 FOBS=     86.82 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  16 FOBS=     86.82 SIGMA=     11.19 
                                                ^^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  17 FOBS=     15.95 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  17 FOBS=     15.95 SIGMA=      5.39 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  18 FOBS=     41.00 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   8  18 FOBS=     41.00 SIGMA=      5.41 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   9   1 FOBS=     13.45 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   9   1 FOBS=     13.45 SIGMA=      1.03 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   9   2 FOBS=     46.05 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   9   2 FOBS=     46.05 SIGMA=      3.00 
                                                 ^^^^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   9   3 FOBS=      9.03 SIGMA= 
                                          ^
 %REFLection-ERR: unrecognized command:
  INDEX=   0   9   3 FOBS=      9.03 SIGMA=      1.10 
                                                 ^^^^
 %PARSER-ERR: Too many parsing errors --> termination
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating

--------------------------------------------------------------------

Here are the first records in the reflection file:

--------------------------------------------------------------------


 NREFlections=    19647
 ANOMalous=FALSE
 DECLare NAME=FOBS         DOMAin=RECIprocal   TYPE=COMP END 
 DECLare NAME=SIGMA        DOMAin=RECIprocal   TYPE=REAL END 
 INDEX=   0   2   3 FOBS=      4.38 SIGMA=      1.38
 INDEX=   0   3   1 FOBS=      3.05 SIGMA=      0.93
 INDEX=   0   3   3 FOBS=     19.01 SIGMA=      2.11
 INDEX=   0   4   1 FOBS=     25.34 SIGMA=      2.29
 INDEX=   0   4   3 FOBS=      9.89 SIGMA=      1.42
 INDEX=   0   5   1 FOBS=     11.76 SIGMA=      0.83
 INDEX=   0   5   3 FOBS=      9.10 SIGMA=      1.24
 INDEX=   0   5   5 FOBS=     13.43 SIGMA=      1.19
 INDEX=   0   5   7 FOBS=      6.95 SIGMA=      2.04
 INDEX=   0   5   8 FOBS=    103.75 SIGMA=     10.95
 INDEX=   0   6   0 FOBS=     36.97 SIGMA=      4.05
 INDEX=   0   6   1 FOBS=     12.63 SIGMA=      0.83
 INDEX=   0   6   2 FOBS=     47.62 SIGMA=      3.52
 INDEX=   0   6   3 FOBS=      8.57 SIGMA=      0.81
 INDEX=   0   6   4 FOBS=     79.34 SIGMA=      8.04
 INDEX=   0   6   5 FOBS=      8.44 SIGMA=      0.87
 INDEX=   0   6   6 FOBS=     92.02 SIGMA=      9.26
 INDEX=   0   6   7 FOBS=     11.85 SIGMA=      2.05
 INDEX=   0   6   8 FOBS=     69.23 SIGMA=      7.97
 INDEX=   0   7   1 FOBS=     14.49 SIGMA=      1.01
 INDEX=   0   7   2 FOBS=     14.26 SIGMA=      1.17
 INDEX=   0   7   3 FOBS=      6.96 SIGMA=      0.95
 INDEX=   0   7   4 FOBS=     32.88 SIGMA=      2.18
 INDEX=   0   7   5 FOBS=      2.02 SIGMA=      1.46
 INDEX=   0   7   6 FOBS=     78.84 SIGMA=      6.15
 INDEX=   0   7   7 FOBS=     11.78 SIGMA=      1.63
 INDEX=   0   7   8 FOBS=    116.28 SIGMA=     13.49
 INDEX=   0   7   9 FOBS=     10.69 SIGMA=      2.54
 INDEX=   0   7  12 FOBS=    113.11 SIGMA=     11.80
 INDEX=   0   7  13 FOBS=     18.42 SIGMA=      3.68
 INDEX=   0   7  14 FOBS=     22.24 SIGMA=      3.81
 INDEX=   0   8   1 FOBS=     18.89 SIGMA=      1.23
 INDEX=   0   8   2 FOBS=     59.91 SIGMA=      3.75
 INDEX=   0   8   3 FOBS=      7.11 SIGMA=      1.10
 INDEX=   0   8   4 FOBS=    100.92 SIGMA=      7.32
 INDEX=   0   8   5 FOBS=      4.15 SIGMA=      1.25
 INDEX=   0   8   6 FOBS=    119.12 SIGMA=     12.43
 INDEX=   0   8   7 FOBS=     20.38 SIGMA=      2.50
 INDEX=   0   8   8 FOBS=    202.38 SIGMA=     20.71
 INDEX=   0   8   9 FOBS=     10.63 SIGMA=      1.99
 INDEX=   0   8  10 FOBS=    117.24 SIGMA=     13.30
 INDEX=   0   8  12 FOBS=    115.82 SIGMA=     12.50
 INDEX=   0   8  13 FOBS=     12.10 SIGMA=      4.05
 INDEX=   0   8  15 FOBS=      8.05 SIGMA=      8.56
 INDEX=   0   8  16 FOBS=     86.82 SIGMA=     11.19
 INDEX=   0   8  17 FOBS=     15.95 SIGMA=      5.39
 INDEX=   0   8  18 FOBS=     41.00 SIGMA=      5.41
 INDEX=   0   9   1 FOBS=     13.45 SIGMA=      1.03
 INDEX=   0   9   2 FOBS=     46.05 SIGMA=      3.00
 INDEX=   0   9   3 FOBS=      9.03 SIGMA=      1.10

-------------------------------------------------------------------

Finally, here is the input file:

-------------------------------------------------------------------


 remarks  file  xtal_maps/map.inp 
 remarks  compute electron density maps of the type  ( a Fobs - b Fobs )
               
{===>} structure @yeei_3.psf  end                        { read structure file }

{===>} coor @yeei_b3a.pdb     end                      
                                                         { read coordinates    }

{{===>}      @ortho.fix                                  { put coordinates into }} 
                                                    { X-PLOR orthogonalization } 
                                                                { convention   }
                                             
 xrefine 
                                  
{===>}
                                   

   a=33.023 b=54.102 c=57.530 alpha=90.0 beta=99.60 gamma=90.

{===>}
   symmetry=(x,y,z)                  {*Symmetry operators for crystal P2(1)   *}
   symmetry=(-x,y+1/2,-z)                

   SCATter ( chemical C* ) 
      2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
   SCATter ( chemical N* )
      12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529
   SCATter ( chemical O* )
      3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800
   SCATter ( chemical S* )
      6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900
   SCATter ( chemical P* )
      6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645 1.11490
   SCATter ( chemical FE* )
      11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566 0.97070
 
{===>} 
   nreflections=50000
   reflection @yeei.xpl      end                            { read reflections }

{===>}   
   resolution   5.0 1.80                                   { resolution range  }

   do amplitude ( fobs = fobs * heavy(fobs - 0.2*sigma))       { sigma cutoff }
   fwind=0.1=100000

   method=FFT          
   
   fft 
      memory=1000000   
   end                 
      

 end                  

xrefin
   mbins=20
   resolution   5.0 1.8                                   { resolution range  }
   update                                    { Compute FCALCS                 }
   do scale ( FCALC = FOBS )                 { FCALCS will be scaled to FOBS  }
   print R
   print comp
   do amplitude (FCALC = FCALC )             { this is for a     fc   map     }
                                             { any other combination of       }
                                             { coefficients may be used.      }

{===>}

   write reflection FOBS SIGMA FCALC  output=yeei.xfc        
                                             { Output file                    }


    end                                      

 end


 stop

--------------------------------------------------------------------

Thanks in advance for any suggestions.

Joseph 

--
--------------------------------------------------------------------
Joseph Nachman				Department of Biochemistry
nachman at hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
--------------------------------------------------------------------



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