Other information listed in the logfile box3d.log includes integrated intensities, averaged 3D profiles, 3D profiles at various parts on a detector, etc.

If the diagnostic level is set x ≥ 2, 3D pixel intensities for each reflection are shown in the log file (see below).

  -2   8 -11   47833.8  287.8  319.7  181.5  -68.7  320.1  181.4  -68.8 3 0
 Rocking curve:  102:2986  103:42587  104:2261

Linear pixel intensity
sampling: 1,  divided: 10
z=102
  3   6   4   4   7   6   3   5   5   4   3   4   5   5   4   4   3   5 
  3+  3+  5+  4+  4+  3+  2+  3+  4+  4+  4+  4+  3+  3+  3+  3+  4+  5+
  4+  5+  6+  5+  5+  4+  4+  4+  4+  4+  5+  4+  4+  4+  2+  3+  4+  5+
  2+  3+  3+  5+  6+  7*  7.  3.  6.  4.  3.  4.  5+  7*  4+  3+  4+  3+
  6+  4+  4+  2+  5.  5.  6.  5.  6.  5.  4.  6.  6.  6.  5+  3+  5+  3+
  3+  2+  4+  4+  6.  2.  3.  4.  5.  6.  4.  4.  6.  5.  5.  3+  5+  3+
  4+  4+  4+  4.  5.  4.  4.  6.  8.  7.  6.  5.  5.  3.  4.  3+  4+  5+
  3+  3+  6+  4.  5.  3.  6.  5.  5.  5.  7.  6.  6.  4.  4.  4.  3+  4+
  3+  3+  3.  5.  5.  4.  5.  7.  5.  7.  8. 11.  9.  8.  6.  4.  3+  6+
  3+  2+  3.  5.  6.  5.  5.  2.  6.  5. 12. 23. 27. 18.  7.  5.  7+  6+
  3+  3+  4+  4.  5.  4.  4.  6.  5.  7.  8. 15. 26. 19.  7.  7.  6+  7+
  5+  4+  4+  5.  5.  5.  3.  3.  6.  5.  5. 12. 13. 12. 10.  7*  8* 10*
  4+  4+  6+  5.  4.  4.  3.  5.  7.  9.  7.  6.  8.  9.  5.  5+  8*  8*
  3+  3+  3+  4+  5.  3.  3.  3.  6.  6.  3.  4.  5.  6.  6+  5+  6+  6+
  2+  3+  4+  4+  3+  4+  4.  4.  4.  5.  5.  3.  4.  3+  4+  5+  4+  4+
  2+  2+  3+  5+  5+  6+  5+  4+  3+  5+  5+  4+  3+  2+  3+  4+  2+  4+
  3+  2+  3+  5+  5+  4+  4+  4+  3+  3+  6+  3+  3+  2+  2+  5+  2+  4+
  3   2   4   5   5   5   4   4   5   5   5   3   4   6   3   3   4   3 
z=103
  2   6   5   4   4   3   6   5   5   6   6   5   4   5   5   4   4   3 
  4+  4+  3+  4+  5+  3+  3+  5+  6+  5+  5+  5+  3+  3+  4+  3+  4+  3+
  4+  4+  5+  4+  8*  6+  6+  5+  6+  4+  5+  4+  4+  5+  4+  3+  4+  4+
  4+  5+  6+  8*  6+  6+ 10.  9.  7.  7.  5.  6.  6+  7+  5+  3+  3+  4+
  7+  4+  6+  6+  6.  6.  8. 11. 10. 10.  8.  7.  9.  6.  5+  3+  4+  4+
  5+  3+  5+  5+  9.  7. 10. 15. 16. 17. 14. 10. 11.  8.  6.  6+  4+  5+
  5+  3+  6+  5.  6.  9. 16. 25. 44. 42. 31. 18. 12. 11.  8.  7+  6+  6+
  4+  3+  7+  7.  6. 12. 27. 75.143.148.113. 59. 23. 12.  7.  6.  5+  4+
  5+  8*  4.  7.  7. 16. 43.129.233.286.243.138. 61. 19.  7.  4.  4+  3+
  3+  4+  5. 11. 11. 17. 40.112.220.300.266.153. 69. 18.  7.  4.  4+  3+
  5+  5+  5+  6.  9. 11. 20. 54.125.190.162.110. 46. 16.  8.  6.  5+  6+
  4+  3+  4+  7.  6.  8. 11. 21. 47. 57. 59. 48. 19. 10.  6.  5+  4+  5+
  3+  2+  7+  8.  6.  6. 10. 12. 18. 17. 21. 17. 10.  8.  7.  6+  5+  6+
  3+  3+  5+  5+  6.  6.  8.  8.  7. 11.  9. 12.  7.  9.  6+  4+  4+  4+
  3+  3+  5+  4+  5+  4+  5.  6.  6.  8.  7.  6.  6.  3+  4+  9*  5+  4+
  5+  5+  4+  6+  5+  6+  6+  4+  4+  6+  7+  7+  6+  4+  5+  7+  3+  5+
  4+  4+  3+  4+  3+  4+  4+  3+  5+  4+  7+  6+  5+  4+  6+  8*  4+  4+
  5   5   4   4   4   5   4   4   6   6   5   5   7   5   5   3   4   4 
z=104
  3   3   3   4   6   4   5   4   5   6   4   4   3   3   4   3   4   3 
  3+  2+  2+  2+  4+  3+  5+  3+  4+  5+  5+  5+  2+  4+  4+  3+  3+  2+
  4+  3+  3+  3+  5+  4+  4+  3+  3+  4+  5+  5+  4+  3+  3+  4+  3+  3+
  3+  2+  3+  4+  5+  3+  5.  3.  3.  5.  4.  3.  3+  5+  3+  3+  3+  4+
  6+  4+  5+  3+  5.  5.  5.  5.  6.  6.  4.  3.  3.  4.  4+  2+  3+  4+
  6+  9*  7+  7+  8.  5.  4.  6.  8.  5.  4.  2.  3.  2.  2.  4+  5+  4+
  6+  9* 10*  9. 11. 11. 11. 10.  7.  5.  5.  4.  3.  4.  5.  5+  5+  4+
  4+  6+ 12* 12. 12. 13. 11.  6.  6.  7.  6.  6.  4.  5.  5.  5.  4+  2+
  6+  5+  5.  7.  9. 11. 13. 10.  7. 10.  6.  6.  3.  2.  5.  6.  4+  3+
  4+  3+  6.  6.  7.  8. 10.  5.  7.  6.  5.  4.  2.  3.  5.  3.  3+  2+
  4+  4+  5+  4.  6.  6.  5.  7.  8.  8.  6.  4.  6.  4.  2.  3.  3+  4+
  4+  4+  4+  4.  6.  3.  3.  6.  9.  7.  3.  5.  5.  5.  4.  3+  5+  2+
  3+  4+  6+  5.  5.  5.  5.  6.  5.  8.  7.  5.  6.  4.  3.  4+  3+  3+
  4+  4+  5+  5+  6.  5.  6.  6.  6.  6.  5.  5.  4.  2.  5+  3+  3+  4+
  4+  6+  5+  4+  4+  6+  4.  4.  4.  5.  4.  3.  4.  3+  6+  6+  3+  3+
  5+  6+  5+  6+  5+  4+  5+  4+  3+  3+  3+  4+  6+  3+  3+  5+  3+  4+
  3+  4+  4+  4+  5+  4+  5+  4+  5+  3+  4+  4+  4+  2+  3+  5+  4+  4+
  3   3   4   4   3   4   4   5   4   3   3   4   4   3   4   4   4   2 

[input files]

• resource.dat
• spot position files
• frame files

[output files]

• logfile: box3d.log
• intensity file(s): image frame + ".fsq". See here for the format of the intensity file.

Back to program table

2.4.3 fs_lsq

In the intensity file, observed positions (X,Y,ω) are recorded. Using the observed (X,Y,ω), the fs_lsq program carries out refinement of the unit-cell parameters (and others) by the least-squares method, with the residual in the form of
   
where (X,Y,ω) are 3D spot coordinates.
The refinable parameters and their brevity codes are the same as those explained in the refinement list of the file resource.dat. They are reproduced here for convenience.

  "List of refinement parameters" is a list of brevity codes, indicating
  parameters to be refined in the refinement cycle. The brevity codes are
  CELL | ROT | DSHIFT | DIST | CENT | DROT | SROT | RADIUS | WAVE.
  These codes (comma-separated, no space) are allowed in the List of 
  refinement parameters.

  CELL     Unit cell parameters, a,b,c,αβγ. Number of free
                 variables depends upon symmetry of unit cell.
  ROT      Crystal rotation angles, φx,φy,φz.
  DSHIFT   Detector shift parameters, Dx,Dy,Dz
  DIST     Refine Dz separately, of 3 parameters of DSHIFT
  CENT     Refine Dx and Dy only, of 2 parameters of DSHIFT
  DROT     Detector rotation angles, Dα, Dβ, Dγ.   
  SROT     Source rotation angles, s0α,s0β,s0γ. 
  RADIUS   Cylinder radius when cylindrical detector is used
  WAVE     Wavelength (not advised except for synchrotron source with ambigious wavelength)

Goniometer angles and offsets have been recently added as refinable parameters.

  GONIO-OMEGA-OFFSET   Crystal goniometer ω offset value
  GONIO-OMEGA-ALPHA    Crystal goniometer ω axis rotation angle
  GONIO-CHI-OFFSET     Crystal goniometer χ offset value
  GONIO-CHI-ALPHA      Crystal goniometer χ axis rotation angle
  GONIO-PHI-OFFSET     Crystal goniometer φ offset value
  GONIO-PHI-ALPHA      Crystal goniometer φ axis rotation angle
  GONIO-2THETA-OFFSET  Detector goniometer 2θ offset value
  GONIO-2THETA-ALPHA   Detector goniometer 2θ axis rotation angle

[option]
 
-n n1 n2 -fsq -ascii -binary -index -index_limit limit -c c -f f -p parameter_list -pl pl -al al -pw pw -aw aw -r r -i i -delta delta -s s -indphi width -x x -h

-n n1 n2:

Frame range. Because the refinement is based on the observed 3D positions (X,Y,ω), the observed 3D information must be prepared before execution.

-fsq -ascii -binary -index:

These keys specify the source of the (X,Y,ω) parameters.

-fsq:

indicates that the 3D source is the spot intensity files. The option "-fsq" is not advised; instead the similar program fs_refine is recommended.

-ascii:

indicates that the3D source is the merged intensity file. When none of these options are given, the default 3D source is the merged file.

-binary:

indicates that the 3D source is the binary intensity file generated by the wide-slice program package.

-index:

indicates that the3D source is the peak file peaks.dat.

-index_limit limit;

When the 3D source is the peak file, it contains observed (X,Y,ω) but no Miller indices. The Miller indices must be converted from their reciprocal coordinates (X,Y,ω). The calculated Miller indices must be integers. For any HKL, if
  |H - nearest integer of (H)| > limit,
the program considers this indexing wrong and rejects the reflection from the LS calculation. The defalt value of "limit" is 0.3.

-c c:

Number of refinement cycles. Default is 10.

-f f:

The program fs_lsq avoids divergence of the least-squares calculation by use of an "eigenvalue filtering technique". This option determines the filtering threshold. If eigenvalue < c*maximum_eigenvalue, then filtering-out the eigenvalue. Default value is 1.0x10^-6.

-p parameter_list:

Specify the parameters to be refined by the brevity codes. Default parameter list is "CELL,ROT,CENT,DIST,DROT,SROT".

-pl pl:

Tolerance value, in mm, of the difference between the observed and the calculated spot position. When |X_obs-X_calc| > pl or |Y_obs-Y_calc| > pl, the the reflection is rejected from the LS calculations. Default value is the averaged spot size written in the resource.dat file.

-al al:

Angular tolerance in ° units. When |ω_obs-ω_calc| > al, the reflection is rejected. Default value is 1°.

-pw pw:

Initial weight of the positional part in the residual expression. I.e. w_X = w_Y = pw. The weights, w_X and w_Y, are reset every cycle to maintain χ² = 1.0. Default value is 1.

-aw aw:

Initial weight of the angular part in the residual expression. I.e. w_ω = aw. The weight is reset every cycle to maintain χ² = 1.0. Default value is 1.

-r r:

Resolution limit in Å. By default, all reflections are used.

-i i:

Inner resolution limit in Å. By default, all reflections are used.

-h h:

In the program fs_lsq, the derivatives required for generating the normal matrix are approximated by the numerical differentials. This option sets the infinitesimal number in the numerical differentials. Default value is 1x10^-6.

-s s:

Sigma cut-off for reflection rejection. When F² < σ(F²)*s, then the program rejects the reflection. Default value is 3.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

-indphi width:

By default, the crystal orientation angles are constant and independent from the frame numbers. The "-indphi" option indicates that the crystal orientation angles vary depending upon the frame numbers. The parameter "width" indicates the number of constant frame numbers. I.e. if width = 5, the crystal orientation angles will change every 5 frames. Default value of 0 indicates constant crystal orientations.

[example output]

> fs_lsq -n 1 50
Least Squares Refinement   March 2001 T Higashi
-------------------------------
  Last update: October 2003: T. Higashi & A. Himeda
parameters to be refined: cell, rot, cent, dist, drot, srot
cycle:1  rms:0.025mm 0.036deg  accepted:435  rejected:11  residual:42391.2
cycle:2  rms:0.023mm 0.053deg  accepted:435  rejected:7  residual:1616.71
cycle:3  rms:0.025mm 0.034deg  accepted:435  rejected:7  residual:1225.4
cycle:4  rms:0.024mm 0.041deg  accepted:435  rejected:7  residual:1351.44
cycle:5  rms:0.026mm 0.033deg  accepted:435  rejected:7  residual:1244.38
cycle:6  rms:0.025mm 0.036deg  accepted:435  rejected:7  residual:1277.38
cycle:7  rms:0.026mm 0.033deg  accepted:435  rejected:7  residual:1252.47
cycle:8  rms:0.025mm 0.034deg  accepted:435  rejected:7  residual:1260.47
cycle:9  rms:0.026mm 0.033deg  accepted:435  rejected:7  residual:1256.04
cycle:10  rms:0.026mm 0.033deg  accepted:435  rejected:7  residual:1257.51
--------------------------------------------
parameters after refinement
cell:   5.12919  14.02424  14.83000  89.7718  89.9429  89.9826
err :   0.00119   0.00336   0.00631   0.0184   0.0168   0.0062
phixyz: 0.4500 -0.3127 172.5049
detector shift vector: -0.5345 -0.2853 0.6363
detector setting angle: 0.2962 -0.0607 -0.2192
source   setting angle: 0.0000 0.0819 0.0000
--------------------------------------------

[input files]

• resource.dat
• spot position files (-fsq), merge file (-ascii), or peak file (-index)

[output files]

• resource.dat (updated with refined parameters)
• frame.dat
• lsq.log

Back to program table

2.4.4 fs_merge

Merge a series of intensity files and generate a merged file. In the merged file, reflections are sorted in terms of Miller indices in an asymmetric unit.

[options]
 
-n n1 n2 -s s -m m -x x -h

-n n1 n2:

Frame number range to be merged.

-s s:

Define space group. The space group is used to transform the Miller indices to the asymmetric unit. Default space group is generated by the combination of lattice type and Laue class written in resource.dat.

-m m:

Define merge filename. Default is that written in resource.dat.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

[example output]

> fs_merge -n 1 720

Cyti_d50t300001.fsq merged ( 14 refs)
Cyti_d50t300002.fsq merged ( 7 refs)
    [etc...]
Cyti_d50t300719.fsq merged ( 9 refs)
Cyti_d50t300720.fsq merged ( 2 refs)
Exclude Duplicated reflections
  9 duplicated reflections were deleted
  Old number of reflections: 6348
  New number of reflections: 6339
merge file generated: Cyti_d50t300.amer ( 6339 refs)

[input files]

• resource.dat
• intensity files

[output files]

• frame.dat
• merge.log
• merge file. For the file format of the merge file, see here.

Back to program table

2.4.5 fs_scale

Calculate frame scale factors, which are in the form:
  
where K_i is the scale factor of the i-th frame group and B_i is the temperature factor. For small-molecule crystallography, the temperature factor is normally not used.

Intensity is scaled as
  
The scale factors and the temperature factors are saved in the supplemental file scan.dat.

[options]
 
-a -w w -r r -c c -tf -fixtf -s s -l l -t t -f f -re -m m -norej -loc - x x

-a:

include consideration of anomalous dispersion. I.e. F²(+) and F²(-) will be treated separately. Since the effect is space group (or more strictly point group) dependent, be sure that the correct space group (or point group) is specified when the merge file is generated. By default, the anomalous effect is not considered.

-w w:

Number of frames in a batch (and therefore having the same scale factor). By default, the number of frames per batch is adjusted to correspond to 5° of oscillation.

-r r:

Resolution limit in Å. By default, use all recorded reflections.

-c c:

Number of refinement cycles. Default is 5.

-tf:

Include refinement of the temperature factor B_i. The default for small-molecule processing is to fix the temperature factor.

-fixtf:

Fix the temperature factors. The default for macromolecular samples is to refine the temperature factors.

-s s:

Set the sigma cut-off value. If F² < s.σ(F²), then that reflection is not used for scaling. Default value is 3.

-l l:

Threshold of small eigenvalues to be filtered. Any eigenvalue < l.(maximum eigenvalue) is filtered. Default value is 1x10^-6.

-t t:

Convergence criterion. When |Δp| < t.σ(p) for all parameters, the program assumes that the least-squares calculation has converged. Default value is 0.05.

-f f:

Scale factor of frame number f will be fixed in the least-squares calculations. By default, no scale factors are fixed.

-re:

Reset all scale factors to 1.00 before the least-squares calculation. By default, do not reset.

-m m:

Name for merge file. By default, the name given in resource.dat as "present merge file" is used.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

[example output]

> fs_scale
Frame Scaling     March 2001 T Higashi
-------------------------------

 Modification of standard error
 |<I>-I|/<sig> = 0.01000+0.081<I>^0.605
17 outliers rejected
cycle:1 Rvalue: 3.421 Residual: 1.2763e+006 used:4731 independent:2323
cycle:2 Rvalue: 2.403 Residual: 3.2154e+005 used:4731 independent:2323
cycle:3 Rvalue: 2.398 Residual: 3.2076e+005 used:4731 independent:2323
cycle:4 Rvalue: 2.398 Residual: 3.2076e+005 used:4731 independent:2323

converged at cycle 4. maximum shift/sigma = 0.000317

[input files]

• resource,dat
• merge file
• frame.dat

[output files]

• scale.log
• frame.dat

Back to program table

Apply an empirical absorption correction. Transmission factors are approximated by a Fourier series and the Fourier coefficients are determined by a least-squares method.

The explicit expression of the transmission factors is:
 
  
  
  
  
The residual of the least-squares calculation is:
 
  
  
where

	Bragg angle
	latitide and longitude of the primary (incident) beam
	latitide and longitude of the secondary (diffracted) beam
	Fourier coefficients to be determined
	i-th individual intensity with Miller indices h
	absorption free intensity with Miller indices h, approximated by average

Normally, the Fourier terms to be considered are:

 Number of A0 terms: 0
 Number of As terms: 17
 n: 1 2 3 4 5 6 0 0 0 0 1 2 3 4 2 3 4
 m: 0 0 0 0 0 0 1 2 3 4 1 1 1 1 2 3 4

 Number of Ap terms: 17
 n: 1 2 3 4 5 6 0 0 0 0 1 2 3 4 2 3 4
 m: 0 0 0 0 0 0 1 2 3 4 1 1 1 1 2 3 4

The basic assumption is that intensity variation among equivalent reflections is due to absorption. Absorption is a slowly-varying function, so that it can be approximated by a relatively low-order Fourier series. In order to determine the Fourier coefficents, a certain number of equivalent reflections must be observed.

In above equations, the term A₀(θ) (the theta-dependent absorption term) cannot be evaluated by the present assumption, because it is isotropic and only dependent on the with Bragg angle. Bragg angles of equivalent reflections are of course equal.

The idea of this calculation comes from the following two papers:
D. Stuart & N. Walker (1979). Acta Cryst. A35, 925.
N. Walker & D. Stuart (1983), Acta Cryst. A39, 158.

[options]
 
options: -a -r r -c c -s s -l l -t t -nop -m m -x x -h

-a:

Include consideration of anomalous dispersion. I.e. F²(+) and F²(-) will be treated separately. Since the effect is space group (or more strictly point group) dependent, be sure that the correct space group (or point group) is specified when the merge file is generated. By default, the anomalous effect is not considered.

-r r:

Resolution limit in Å. By default, use all the recorded reflections.

-c c:

Number of refinement cycles. Default is 5.

-s s:

Set the sigma cut-off value. If F² < s.σ(F²), then the reflection is not used to determine the absorption parameters. Default value is 3.

-l l:

Threshold of small eigenvalues to be filtered. Any eigenvalue < l.(maximum eigenvalue) is filtered. Default value is 1x10^-6.

-t t:

Convergence criterion. When |Δp| < t.σ(p) for all parameters, the program assumes that the least-squares calculation has converged. Default value is 0.05.

-nop:

Ignore the ν_p contribution to the absorption effect. If the data were collected by rotation about only one axis, ν_p must be zero. If the -nop option is not selected and the variation of ν_p is small, this contribution is automatically ignored.

-m m:

Input merge file name. By default, the name given in resource.dat as "present merge file" is used.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

[example output]

> fs_abscor
Empirical Absorption Correction   March 2001 T Higashi
-------------------------------

 Modification of standard error
 |<I>-I|/<sig> = 0.01000+0.191<I>^0.477
17 outliers rejected

 Absorption coeffient terms

 A0 terms: 0    As terms: 17    Ap terms: 17

 independent reflections: 2323
 total observations: 4731
 averaged intensity: 3591.08

cycle 1: R factor= 2.407,Residual= 3.2376e+005
cycle 2: R factor= 2.310,Residual= 2.9572e+005
cycle 3: R factor= 2.132,Residual= 2.5224e+005
cycle 4: R factor= 2.132,Residual= 2.5223e+005

Maximum and minimum absorption factors(normalized):   1.000   0.768
merge file generated: Cyti_d50t300.amer ( 6339 refs)

[input files]

• resource.dat
• merge file
• frame.dat

[output files]

• abscor.log
• merge file.    Final absorption factors are stored in the merge file.

Back to program table

2.4.7 fs_laue

Determination of Laue class.

1. The program analyzes the unit-cell parameters and extracts possible Bravais lattices.
2. The symmetry of the intensity distribution is examined for each of the Bravais lattice candidates.
3. The highest symmetry class that meets the input criteria is selected as the Laue class.

The following three statistical values are calculated for symmetry judgement.
  
  
  
where suffixes i & j indicate two groups of reflections related by a symmetry element, e.g. two-fold axis.

[options]
 
-r r -s s -n n -R R -c1 c1 -c2 c2 -x x -dl dl -da da -dg dg -x x -h

-r r:

Resolution limit in Å unit. By default, use all the recorded reflections.

-s s:

Sigma cut-off value. Reflections having F² < s.σ(F²) are not used to evaluate the Laue class. Default value is 3.

-n n:

Minimum acceptable number of reflections in a group. Default value is 3.

-R R:

R-value threshold. Accept Laue symmetry if R-value < R. Default value is 10.0

-c1 c1:

Correlation threshold. Accept the Laue symmetry if correlation > c1. Default value is 0, i.e. the correlation value is not used to determine Laue symmetry.

-c2 c2:

Threshold of type2 correlation. Default value is 0.95.

The symmetry is determined when all of the three criteria (R, c1, c2) are satisfied.

The next three values are used for the cell reduction step executed prior to the Laue class check.

-dl dl:

Cell length tolerance in Å. Default is 0.5Å.

-da da:

Cell angle tolerance in ° . Default is 1.2°.

-dg dg:

Tolerance value for the elements of metric tensor G. By default, an appropriate value calculated from the "dl" and "da" values is used.

-m m:

Input name of merge file. By default, the name given in resource.dat as "present merge file" is used.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

[example output] Part I
 
Before higher symmetries are tested, outlier reflections are rejected assuming current space group P-1. The first candidate in the example is possibly tetragonal. Two possible Laue classes are examined, and fail.

> fs_laue
Laue Class     March 2001 T Higashi
-------------------------------

 Modification of standard error
 |<I>-I|/<sig> = 0.01000+0.205<I>^0.45
16 outliers rejected

----------------- Current Cell -------------
crystal system: Tetragonal  lattice type: P
 cell: 14.05200 14.82700 5.13000 89.9900 89.9800 89.8900

 Laue groups to be checked are:  4/mmm 4/m

 number of total reflections          =  6052
 number of refs with non-zero indices =  4835
 number of refs with zero indices     =  1217
 minimum and maximum index H          =   -16    14
 minimum and maximum index K          =   -17    16
 minimum and maximum index L          =    -6     6

 Laue symmetry statistics

   n      symmetry      pairs      <FSQ>    R-val(%) corr 1    corr 2
 -------------------------------------------------------------------
   1      -h,-k,-l        791      3546       2.2   0.99925   0.99942  OK
   2      -h,-k,+l       3691      3512       3.8   0.99690   0.99746  OK
   3      -h,+k,+l       4151      3320       3.4   0.99682   0.99737  OK
   4      +h,-k,+l       3792      3500       3.3   0.99740   0.99787  OK
   5      +k,-h,+l       7082      3324      47.5   0.34656   0.45918
   6      -k,+h,+l          0         0       0.0   0.00000   0.00000  ??
   7      +k,+h,+l       3490      3332      47.6   0.34323   0.45772
   8      -k,-h,+l       3541      3323      47.3   0.35022   0.46207

   n      symmetry      pairs      <FSQ>    R-val(%) corr 1    corr 2
 -------------------------------------------------------------------
   1         4/mmm      26538      3382      26.4   0.65315   0.71420
   2           4/m      11564      3399      29.8   0.60099   0.67180

 Failed to determine an appropriate Laue group.

[example output] Part II
 
The next possible symmetry is orthorhombic. Laue class mmm is examined and is found to be correct.

----------------- Current Cell -------------
crystal system: Orthorhombic  lattice type: P
 cell: 5.13000 14.05200 14.82700 89.8900 89.9900 89.9800

 Laue groups to be checked are:  mmm

 number of total reflections          =  6052
 number of refs with non-zero indices =  4835
 number of refs with zero indices     =  1217
 minimum and maximum index H          =    -6     6
 minimum and maximum index K          =   -16    14
 minimum and maximum index L          =   -17    16

 Laue symmetry statistics

   n      symmetry      pairs      <FSQ>    R-val(%) corr 1    corr 2
 -------------------------------------------------------------------
   1      -h,-k,-l        790      3550       2.2   0.99925   0.99942  OK
   2      -h,-k,+l       3790      3502       3.3   0.99729   0.99776  OK
   3      +h,-k,-l       3690      3513       3.8   0.99702   0.99755  OK
   4      -h,+k,-l       4150      3321       3.4   0.99685   0.99740  OK

   n      symmetry      pairs      <FSQ>    R-val(%) corr 1    corr 2
 -------------------------------------------------------------------
   1           mmm      12420      3448       3.4   0.99714   0.99765  OK

 Laue group is determined to Pmmm

 Original crystal system = triclinic
 Original lattice type   = P
 Original Laue class     = -1
 Original cell parameters = 5.130 14.052 14.827 89.89 89.99 89.98

 Final crystal system = Orthorhombic
 Final lattice type   = P
 Final Laue class     = mmm
 Final cell parameters = 5.130 14.052 14.827 89.89 89.99 89.98

 Axis Transformation
Cell parameters and reflection indices are identical

Old lattice type, Laue class & Crystal system: P -1 triclinic
New lattice type, Laue class & Crystal system: P mmm orthorhombic
merge file generated: Cyti_d50t300.amer ( 6339 refs)
 Merge file : Cyti_d50t300.amer has been changed.

[input files]

• resource.dat
• merge file
• frame.dat

[output file]

• laue.log
• resource.dat

Back to program table

2.4.8 fs_final

This program is designed to perform the last steps of data processing, i.e. reject outliers, adjust sigmas and output data.

Functions:

1. Reject outlier reflections.
2. Assess the variance of equivalent intensities and modify the standard error of each intensity by adjusting the variance.
3. Calculate R-merge and other statistical values and tabulate them.
4. Output intensity data in various formats.
5. For small-molecule data, generate the file "texray.inf".

[options]
 
-a -r r -s s -o o -nom -f f -m m -x x -h

-a:

include anomalous dispersion in the calculations. Ie. F²(+) and F²(-) are treated as different groups. Since anomalous dispersion is point group dependent, the correct point group must be specified when the merge file is generated, otherwise the anomalous effect may not be handled correctly. By default, the anomalous effect is ignored.

-r r:

Resolution limit in Å. By default use all the recorded reflections.

-s s:

Sigmacut value. Reject reflection if F² < s.σ(F²). Default value is -3.

-o o:

Reject reflection if |F²(i) - <F²>| > o.σ[F²(i)]. Default value is 5.0

-nom:

By default the standard error of an intensity, σ[F²(i)], is modified by taking into account the variance in the intensities of equivalent reflections. But if this key is given, the standard error is not modified.

-f f;

The equation to modify the standard error of an intensity is:

   σ(F²)' = [a + b.<F²>^c].(F²)

where a, b and c are constants determined by an analysis of variance for equivalent intensities. When f is given, a in the above equation is replaced with f given here.

-m m:

Input merge filename. By default, the name given in resource.dat as "present merge file".

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

> fs_final
Final Output   March 2001 T Higashi
-------------------------------

 Modification of standard error
 |<I>-I|/<sig> = 0.97529+0.0765<I>^0.579
41 outliers rejected

 Modification of standard error
 |<I>-I|/<sig> = 1.40568+0.0665<I>^0.579

 sigma modification:
    new sigma(F2) = (fudge0+fudge1*(F2)^fudge2)*sigma(F2)
    where fudge0=1.405677, fudge1=0.066465, fudge2=0.578509

Output reflections
 Anomalous dispersion was ignored
 Absorption correction:  Multi-scan
    minimum & maximum transmission factors: 0.733648 1.000000
    oblique incidence correction not applied
 Averaged reflection file: f2.dat
 Averaged Fobs file: fobs.dat
 Individual reflection file: f2plus.dat
 Number of unique reflections: 1172
 Number of accepted reflections: 6295
 Sigmacut rejected: 2,  Outlier rejected: 41
 Rmerge(all ref): 3.088
 Rmerge(1sigma): 3.084
 Rmerge(2sigma): 3.080
 Rmerge(3sigma): 3.071
 Average redundancy: 5.371
 Completeness: 1.000
 Chi-squares: 1.212
 Information File: texray.inf
 Averaged F2 Refelction File: f2.dat
 Individual F2 Refrection File: f2plus.dat
 D*TREK Format Reflection File: dtrek.dat
 SHELX  Format Reflection File: shelx.hkl

[input files]

• resource.dat
• frame.dat
• merge file

[output files]

• final.log
• texray.inf (when sample type is small-molecule).
• f2plus.dat, Rigaku standard reflection file.
• f2.dat, a file of averaged intensities.
• dtrek.dat, a reflection file in D*TREK format.
• shelx.dat, a reflection file in SHELX format.

Back to program table

2.4.9 fs_axis

This routine performs unit cell transformations and updates the resource.dat file (cell parameters) and the merge file (reflection indices), if it exists. The routine does not rewrite positional files or intensity files, so the merge routine should not be used to create a merge file following this transformation. To create new integrated intensities directly, the integration should be performed again.

The orientation matrix is correctly modified to reflect the transformation.

A cell transformation may also require a change in the Laue class or space group, so an option to include the new symmetry information is provided.

[options]

-t t -s s -l l -c c -R -H -m m -x x -h

-t t:

Specify the transformation matrix. For example, if you convert from the hexagonal obverse setting of a rhombohedral lattice to the primitive rhombohedral setting, t must be "2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c". In addition to using a fractional expression, a decimal point expression, such as 0.5a, is allowed. It may be convenient to define some transformations in reciprocal space. Therefore, reciprocal space expressions, e.g. a*+b*, are also supported. Do not include spaces in the transformation matrix, unless the expression is delimited by double quote marks. When "-t t" is not given, do not perform a transformation.

-s s:

Space group symbol of the resulting lattice. By default, keep the present space group.

-l l:

Laue class of the resulting lattice. If the new symmetry is specified by a space group symbol, this Laue class option is not necessary. By default, keep the current Laue class.

-c c:

Specifies the lattice type of the resulting lattice. The value must be one of "P/A/B/C/I/F/R".

-R or -H:

Special case transformations for rhombohedral lattices. -R means conversion from a triple-hexagonal setting to a primitive rhombohedral setting, and -H specifies a transformation from a primitive rhombohedral cell to its triple-hexagonal setting.

-m m:

Explicitly specify the name of the merge file. The default is the systematic name (shown in resource.dat).

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

[example output]

> fs_axis -t b,c,a -s P212121
 Cell Transform: b,c,a
 Transform Matrix: 0 1 0/ 0 0 1 / 1 0 0

 Axis Transformation

old parameters:
 cell:   5.12590  14.04770  14.88900  90.3350  89.9170  89.8373
 err :   0.00490   0.01330   0.02700    0.067    0.063    0.020
 rotation and x-ray axes: +a -b*
 crystal setting angles:    -0.4440    0.3400   -7.4890

new parameters:
 cell:   14.04770  14.88900   5.12590   89.9170   89.8373   90.3350
 err :    0.01330   0.02700   0.00490    0.0630    0.0200    0.0670
 rotation and x-ray axes: +a -b*
 crystal setting angles:   -89.4999    0.4460   82.1784

    symmetry              Old         New
 space group   :      unknown      P212121
 Laue class    :           -1          mmm
 lattice type  :            P            P
 crystal system:    triclinic orthorhombic

merge file generated: Cyti_d50t300.amer ( 6339 refs)
 Merge file : Cyti_d50t300.amer has been changed.

[input files]

• resource.dat

[output files]

• axis.log
• resource.dat
• merge file

Back to program table

2.4.10 fs_reduce

Cell reduction and selection of Bravais lattice. Normally the indexing program fftindex performs the cell reduction and determines an appropriate Bravais lattice. The fs_reduce routine allows the user to manually select the crystal system and lattice type. The modified unit cell parameters, constrained to the chosen crystal system, are written to the resource.dat file. If a merge file exists, the indices are transformed to the new cell setting.

[options]
 
-l l -a a -g g -x x -h -c a b c alpha beta gamma -p p

-l l:

Cell length tolerance in Å. Default is 0.003*(a+b+c)/3, where a, b and c are the unit-cell lengths.

-a a:

Cell angle tolerance in degrees. Default is 0.2 °.

-g g:

Tolerance value for the elements of metric tensor G. By default, an appropriate value is calculated using the above "l" and "a" values.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

-c a b c alpha beta gamma

Cell reduction and Bravais lattice determination depend only upon unit-cell parameters and lattice centering. By default the program reads the resource.dat file to get cell parameters and lattice type. This option allows user input of the cell parameters.

-p p;

Optional input of lattice centering. One of P/A/B/C/I/F/R.

[example output]

> fs_reduce

List of possible conventional cells

  No    System    Cent.     a        b        c      alpha    beta   gamma
   1  Orthorhombic  P      5.130   14.052   14.827   89.89   89.99   89.98
   2  Monoclinic    P      5.130   14.052   14.827   89.89   89.99   89.98
   3  Monoclinic    P      5.130   14.827   14.052   89.89   89.98   89.99
   4  Monoclinic    P     14.052    5.130   14.827   89.99   89.89   89.98
   5  Triclinic     P      5.130   14.052   14.827   89.89   89.99   89.98

 Select the desired cell by No ...
1

 Axis Transformation
 Same unit cell

    symmetry              Old         New
 space group   :      unknown         Pmmm
 Laue class    :           -1          mmm
 lattice type  :            P            P
 crystal system:    triclinic orthorhombic

merge file generated: Cyti_d50t300.amer ( 6339 refs)
 Merge file : Cyti_d50t300.amer has been changed.

[input files]

• resource.dat
• merge file, if it exists

[output files]

• reduce.log
• resource.dat
• merge file, if it exists

Back to program table

2.4.11. fs_integ

This program combines two fundamental routines:

1. generation of reflection positions (fs_gen)
2. estimation of integrated intensities (fs_box3d)

[options]
 
-n n1 n2 -r r -i i -m m -x x -h

-n n1 n2:

Frame range given by frame numbers. Frames from #n1 to #n2 are to be processed.

-r r:

Resolution limit in Å. By default, the resolution limit in resource.dat is used.

-i i:

Inner resolution limit in Å. By default, the resolution limit in resource.dat is used.

-m m:

Effective mosaic spread in °. By default, the value in resource.dat is used.

-x x:

Output diagnostic information. "x" indicates diagnostic level.

-h:

Print a brief explanation of options.

Note. Unlike fs_box3d, the fs_integ has no "-nohb" and no "-ellipse" arguments.

[example output]

> fs_integ -n 100 120

 Frame range: 100 - 120
 ../Cyti_d50t300###.img
 Resolution limit: 0.834 A
   473 spots generated in total
       195 fully recorded
        22 partially recorded
       256 failed outside detector

   198 reflections,  of which
       196 reflections observable
         2 reflections out of detector area

 maximum 3D pixels: 1620
 Background estimation: 2D background
 Background type: rectangle background
total: 196, positive: 187, negative: 4
 underloaded: 5
rms(XY):0.146mm,rms(X):0.099,rms(Y):0.108,rms(omega):0.109deg
: -0.042mm : -0.004mm

[input files]

• resource.dat
• scan.dat

[output files]

• integ.log
• spot position file
• spot intensity file

Back to program table

2.4.12. fs_refine

Combination of 3 fundamental programs:

1. generation of reflections (fs_gen)
2. Evaluation of integrated intensities (fs_box3d)
3. Least-squares refinement (fs_lsq)

This program is useful to refine parameters on a temporary basis. The indexing program fftindx provides only crude crystal orientation information, and no detector parameters are refined. Therefore fs_refine improves these parameters.

[options]
 
Most of the options releted to refinement are common to those of fs_lsq.
 
-n n1 n2 -c c -f f -p parameter_list -pl pl -al al -pw pw -aw aw -r r -i i -delta h -indphi width -x x -h

-n n1 n2:

Frame range.

-c c:

Number of refinement cycles. Default is 5.

-f f:

Eigenvalue filtering threshold. Default is 1 x 10^-6.

-p parameter_list:

List of parameters to refine. Default is "cell,rot,cent,dist,dset,srot".

-pl pl:

-al al:

Length tolerance in mm and angluar tolerance in °. Default of pl is average spot size and that of al is 1°.

-pw pw:

-aw aw:

Initial weight for positional part and angle part. Default values are 1 in both case.

-delta h:

Increment in numerical derivative calculations. Default is 1 x 10^-6.

-r r:

-i i:

Outer and inner resolution limit in Å. By default, the values in resource.dat are used.

-indphi width:

This indicates to use slightly different crystal orientation angles depending upon oscillation angles. "width" is the angular range, defined by frame numbers, with constant crystal orientation angles.

-x x:

Diagnostic print level. Default is 0.

-h:

Print brief description of options.

[example output]
 
This example was done just after fftindex indexing. Root-mean-squares displacements of 0.220mm for position and 0.150deg for the diffraction angle are reduced to 0.029mm and 0.043deg, respectively.

> fs_refine -n 1 20

 Frame range: 1 - 20
 ../Cyti_d50t300###.img
 Resolution limit: 0.834 A
   459 spots generated in total
       189 fully recorded
        18 partially recorded
       252 failed outside detector

   197 reflections,  of which
       189 reflections observable
         8 reflections open backward

 maximum 3D pixels: 1938
 Background estimation: 2D background
 Background type: rectangle background
total: 197, positive: 182, negative: 3
 underloaded: 5
rms(XY):0.330mm,rms(X):0.314,rms(Y):0.102,rms(omega):0.222deg
: -0.274mm : 0.036mm
parameters to be refined: cell, rot, cent, dist, dset, srot
cycle:1  rms:0.220mm 0.150deg  accepted:178  rejected:7  residual:1.04454e+007
cycle:2  rms:0.029mm 0.046deg  accepted:178  rejected:3  residual:71.8592
cycle:3  rms:0.030mm 0.044deg  accepted:178  rejected:3  residual:493.643
cycle:4  rms:0.029mm 0.043deg  accepted:178  rejected:3  residual:468.555
cycle:5  rms:0.029mm 0.043deg  accepted:178  rejected:3  residual:485.897

[input files]

• resource.dat
• scan.dat

[output files]

• refine.log
• resource.dat
• spot position file
• spot intensity file

Back to program table

2.4.13. fs_collect

The program fs_collect was developed for automatic data processing. For example, a set of 720 image frames with two different goniometer settings could be integrated by the command:

    fs_collect -n 1 720 50

The last number in this example indicates that the processing unit is every 50 frames. Flow in this case is as follows;

1. Images are bundled in groups of 50.
2. Repeat refinement steps as given by refinement list in resource.dat.
3. Integrate intensities from these frames and output to the intensity files.
4. Repeat 1-3 until all 720 frames are processed.

A range of images that consists of multiple scans is handled correctly. The end of each scan is detected automatically and contiguous frames are handled correctly.

[options]
 
-n n1 n2 n3 -r r -i i -m m -pf pf -f f -t boxfile -nohb -nolsq -narrow -ellipse -wt str -x x -h

-n n1 n2 n3:

n1 and n2 are start and end image frames to be processed. n3 indicates the number of image frames per bundle. No default is supplied.

-r r -i i:

Outer and inner resolution limits in Å units. By default, values in resource.dat are used.

-m m:

Effective mosaic spread, in degrees. By default, the value in resource.dat is used.

-pf pf:

Cutoff for application of a profile-fitted intensity measurement. Reflections having I/σ(I) less than pf will be profile-fitted. I.e. if I/σ(I) estimated by the simple sum method is smaller that the threshold pf, then the intensity is re-estimated by the profile-fitting method. By default, pf = 6. The local 2D profile is used as a standard 2D profile.

-f f:

Name of spot position files. By default, the standard rule of naming is applied.

-t boxfile:

Name of a scratch file for saving 3D peak intensities. By default, the 3D peak intensities are not saved in the scratch file but are temporarily stored in computer memory.

-nohb:

This indicates that pixels with higher background are not omitted. By default, higher pixel intensities in the background area are not used for background calculation.

-nolsq:

The refinement steps (Flow #2) are not applied. By default, apply.

-narrow:

This indicates "narrow" bundle of frames. Reflections that extend beyond either end of a bundle are so-called "partial reflections" and their rocking curves are extended to the next contiguous bundle. By default, those "partial reflections" are integrated by automatic extension of the bundle. This option turns off the automatic extension of the bundle and therefore integrated intensities of "partial reflections" are not evaluated.

-ellipse:

Use an ellipsoidal background area. For details, see fs_box3d.

-wt str:

Indicates the weighting scheme for least-squares refinement. By default, str = fsq, i.e. the weight of each observation is the intensity of the reflection. Other possible strings are "unit" and "fsq/sig", unit weight and I/σ(I), respectively.

-x x:

Diagnostic print level. Default is 0.

-h:

Print brief description of options.

[example output]

> fs_collect -n 1 720 50

Data Collection     March 2001 T. Higashi
 Last Update        July  2005 T. Higashi
-------------------------------

 Frame range: 1 - 50
 ../Cyti_d50t300###.img
 Resolution limit: 1.500 A
   195 spots generated in total
       106 fully recorded
         4 partially recorded
        85 failed outside detector

   108 reflections,  of which
       104 reflections observable
         4 reflections open backward

 maximum 3D pixels: 3060
 Background estimation: 2D background
 Background type: rectangle background
total: 108, positive: 100, negative: 2
 underloaded: 2
rms(XY):0.048mm,rms(X):0.033,rms(Y):0.035,rms(omega):0.067deg
<X>: -0.011mm <Y>: 0.007mm
parameters to be refined: cent
cycle:1  rms:0.019mm 0.080deg  accepted:99  rejected:3  residual:228169
cycle:2  rms:0.014mm 0.080deg  accepted:99  rejected:2  residual:198.615
cycle:3  rms:0.014mm 0.080deg  accepted:99  rejected:2  residual:291
cycle:4  rms:0.014mm 0.080deg  accepted:99  rejected:2  residual:291
cycle:5  rms:0.014mm 0.080deg  accepted:99  rejected:2  residual:291

-----------------------------
                :
                :
          (syncopation)
                :
                :
 Frame range: 661 - 720
 ../Cyti_d50t300###.img
 Resolution limit: 0.834 A
  1244 spots generated in total
       539 fully recorded
        22 partially recorded
       683 failed outside detector

   544 reflections,  of which
       532 reflections observable
         1 reflections out of detector area
        11 reflections open forward

 maximum 3D pixels: 3060
 Background estimation: 2D background
 Background type: rectangle background
total: 543, positive: 515, negative: 3
 overloaded: 1
 underloaded: 13
rms(XY):0.122mm,rms(X):0.080,rms(Y):0.092,rms(omega):0.087deg
<X>: -0.005mm <Y>: -0.003mm

[input files]

• resource.dat
• scan.dat
• frame files

[output files]

• collect.log
• spot position files
• spot intensity files

Back to program table

2.4.14. fs_spotsize

The fs_spotsize program determines the recommended measurement box size. The fs_gen and fs_box3d programs first collect pixel intensities by assuming an excessively large measurement box. Then, using the "seed-skewness method" [Bolotovsky, White, Darovsky, & Coppens (1995). J. Appl. Cryst. vol 28, 86-95.], the central peak area is extracted and measurement box parameters are determined. The program assumes that refinement calculations have been already carried out to convergence. If not, a larger peak area may be evaluated.

[options]
 
-n n1 n2 -s s -b b -o o -r r -i i -m m -x x -h

-n n1 n2;

Frame range.

-s s:

Excessively large spot area, in mm. Default is 5 mm.

-b b:

Background margin, in mm. Default is 0.3mm.

-o o:

Offset angle to oscillation angles, in degrees. Default is 0.

-r r -i i;

Outer and inner resolution limits, in Å. The default values are those in resource.dat.

-m m:

Effective mosaic spread, in degrees. Default is the value in resource.dat.

-x x:

Diagnostic print level. Default is 0.

-h:

Print brief description of options.

[example output]

> fs_spotsize -n 1 30

Frame range: 1 - 30
../Cyti_d50t300###.img
Resolution limit: 0.834 A
  662 spots generated in total
      281 fully recorded
       16 partially recorded
      365 failed outside detector

  297 reflections,  of which
      268 reflections observable
        4 reflections out of detector area
        9 reflections open backward

   working spot size: 35 x 35
determined spot size: 13 x 13
recommended box size: 17 x 17

[a part of log file]

The upper box is a 2D profile using the larger box and showing adjacent peaks. The lower box is the program-selected measurement box.

working spot size: 35 x 35

 2D profile
sampling: 1,  divided: 10
 6 91111 9 7 6 5 4 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 9121413121110 8 5 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 7111211101011 9 6 4 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 6 7 6 6 7 8 7 5 3 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 3 3 3 3 4 4 4 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 3 3 3 3 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 2 2 2 3 4 5 6 7 6 4 3 3 2 2 2 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 2 2 2 3 4 610161713 8 5 3 2 2 2 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 2 2 2 3 5122647534021 8 4 3 2 2 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 2 2 2 4 719478191733913 6 3 2 2 2 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 2 2 2 4 721528999814516 6 3 2 2 2 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 2 2 2 3 613356374573213 6 3 2 2 2 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 2 2 2 3 4 81530362715 7 4 3 2 2 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 2 2 3 3 5 7111210 7 4 3 2 2 2 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 2 2 2 3 3 4 5 5 5 4 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 3 3 3 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 5 6 5 3 2 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 6 910 9 6 3 2 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 4 7111210 6 3 2 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 6 910 8 5 3 2 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 4 6 6 5 3 2 1 1 1


 determined spot size: 13 x 13
 recommended box size: 17 x 17

 background subtracted
sampling: 1,  divided: 10
 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0+ 0+ 0. 0. 0. 0. 0. 0+ 0+ 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0. 0. 1. 1. 1. 1. 1. 0. 0. 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0. 1. 1. 3. 4. 5. 4. 2. 1. 1. 0. 0+ 0+ 0+
 0+ 0+ 0+ 1. 2. 4. 8.14.15.11. 6. 3. 1. 0. 0+ 0+ 0+
 0+ 0+ 0. 1. 3.10.24.44.51.38.19. 6. 2. 1. 0. 0+ 0+
 0+ 0+ 0. 2. 5.17.45.79.89.71.37.11. 4. 1. 0. 0+ 0+
 0+ 0+ 0. 2. 5.19.50.87.97.79.43.14. 4. 1. 0. 0+ 0+
 0+ 0+ 0. 1. 4.11.33.61.72.55.30.11. 4. 1. 0. 0+ 0+
 0+ 0+ 0. 1. 2. 6.13.28.34.25.12. 5. 2. 1. 0. 0+ 0+
 0+ 0+ 0+ 0. 1. 3. 5. 9.10. 8. 5. 2. 1. 0. 0+ 0+ 0+
 0+ 0+ 0+ 0. 1. 1. 2. 3. 3. 3. 2. 1. 0. 0. 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0. 0. 1. 1. 1. 1. 1. 0. 0. 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0+ 0+ 0. 0. 0. 0. 0. 0+ 0+ 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+
 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+ 0+

[input files]

• resource.dat
• scan.dat
• frame files

[output files]

• spotsize.log
• resource.dat

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2.4.15. fs_mosaic

The program determines an appropriate mosaic spread on the assumption that the image frames have been collected by the fine-slice method, and hence rocking curves are sufficiently observed. Assuming that the rocking curve is a Gaussian function, the program compares the Gaussian function and the observed rocking curves to determine the effective mosaic spread. In order to use this program, image frames must be taken by the fine-slice method, and the unit-cell and crystal orientation should be sufficiently well refined.

Use of this program with wide-slice frames will result in a mosaic spread is not reliable.

[options]
 
-n n1 n2 -r r -i i -c c -x x -h

-n n1 n2:

Frame range.

-r r -i i:

Outer and inner resolution limits in Å. The default values are those in resource.dat.

-c c:

Number of refinement cycles. Default is 5.

-x x:

Diagnostic print level. Default is 0.

-h:

Print brief description of options.

[example output]

> fs_mosaic -n 1 30

Mosaic          June 2001 T Higashi
-------------------------------

 Frame range: 1 - 30
 ../Cyti_d50t300###.img
 Resolution limit: 0.834 A
   674 spots generated in total
       283 fully recorded
        20 partially recorded
       371 failed outside detector

   303 reflections,  of which
       293 reflections observable
        10 reflections open backward

 maximum 3D pixels: 2142
 Background estimation: 2D background
 Background type: rectangle background
total: 303, positive: 287, negative: 0
 underloaded: 6
rms(XY):0.139mm,rms(X):0.109,rms(Y):0.085,rms(omega):0.112deg
: 0.004mm : 0.001mm
 Number of Partial Reflections: 280
 Number of Partially Recorded Fractions: 831
 cycle: 1  mosaic: 0.640(0.015)  residual: 1.037798e+001
 cycle: 2  mosaic: 0.635(0.015)  residual: 1.006429e+001
 cycle: 3  mosaic: 0.634(0.015)  residual: 1.005762e+001
 cycle: 4  mosaic: 0.634(0.015)  residual: 1.005761e+001
 cycle: 5  mosaic: 0.634(0.015)  residual: 1.005761e+001

[input files]

• resource.dat
• scan.dat
• frame files

[output files]

• spotsize.log
• resource.dat

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Files used in the fine-slice programs are tabulated as follows:

3.1. Some comments on files

3.1.1. ASCII format

Most files are now in ASCII format, making them is easy to read with any text editor or browser. Although we have chosen to use an ASCII format, we remind the user of some drawbacks of this format compared to a binary format, i.e. (1) an increase in filesize and (2) a slight decrease in accuracy.

In most of the ASCII files we use a common format, as follows:

1. Caption. A file can be considered a large table; so a brief caption is included on the 1st line of the file.
2. Comment line. If the first character of a line is '#', it is a comment line. The programs ignore the comment line. The caption is also a comment line, so the caption begins with the character '#'.
3. No column adjustment. The ASCII files may not be easy to read because no column adjustment is attempted. This avoids an unnecessary increase in file size due to multiple blank columns.

3.1.2. Special folder "POSFSQ" for position and intensity files

Positional information for spots is saved in a spot position file, and integrated intensity information is in a spot intensity file. The position file and the intensity file have a one-to-one correspondence with the image frame files. If the name of the frame file is "abc001.img", then the positional file and intensity file are "abc001.pos" and "abc001.fsq". For example, if we have 720 image files, we will have 720 positional files and 720 intensity files after processing. (Too many?)

It is convenient to keep the position and intensity files in a special folder. The name of the special folder is "POSFSQ". If a folder named "POSFSQ" exists within a working folder, then the programs will search for the position file or intensity file in the "POSFSQ" subfolder and will save those files in it. This trick helps keep the working folder neat.

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3.2. Indivudual file format

We call a "scan" a series of image frames with constant goniometer angles and crystal-to-detector distance. A rocking curve is recorded on the contiguous frames. Even if the frame ID numbers are contiguous, if their goniometer angles are different, they do not belong to the same "scan" and the rocking curve is never generated. In this sense, "scan" information is important in processing fine-slice frames.

The file scan.dat holds this "scan" information. For example, when fs_integ is executed, the program checks the given frame range, and tests whether the range is within a "scan" by comparing to the scan.dat file. The check should be done in any program related to integration.

The file scan.dat is generated whenever the program finds that there is no scan.dat in the working folder. In this case the program gets goniometer angles, etc, by reading the headers of all image frames to generate the scan.dat file.

A typical scan.dat is shown below:

# first last axis start delta overlap pixelx pixely length records distance radius omega chi phi swing dchi couplex coupley
1 360 omega -120 0.5 0 0.1464 0.1464 512 512 50 0 -120 54 0 -30 0 0 0
361 720 omega -120 0.5 0 0.1464 0.1464 512 512 50 0 -120 54 90 -30 0 0 0

first last

starting and ending frame numbers of the scan.

axis

A string showing the scan axis: "omega" or "phi".

start delta

Starting ω (φ if axis="phi") angle and oscillation width of each frame, in degrees.

overlap

Overlap angle. Should be 0°.

pixelx pixely

Pixel size in mm along x-axis (horizontal-axis) and y-axis (vertical-axis).

length records

Record length in pixels and number of records

distance radius

Crystal-to-detector distance and cylinder radius (when a cylindrical detector is in use). Both in mm.

omega chi phi

Goniometer angles, ω, χ and φ, in degrees.

swing dchi

Detector goniometer angles. 2θ and detector χ in degrees. Detector χ must be 0.

couplex coupley

Coupling constant between crystal rotation and detector movement, in mm/°. These constants are for Weissenberg geometry.

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The values of some parameters may vary with frame number, such as frame scale factors. If we assume that the crystal orientation varies with frame number, frame-specific crystal orientation must be maintained. The frame-dependent values are saved in the file frame.dat. The frame.dat file is normally generated by fs_merge.

A part of frame.dat is shown below:

# No. scan_no. phix phiy phiz scaleF tempF
1 1 -0.499 0.412 -7.605 0.96363 0.00000
2 1 -0.499 0.412 -7.605 0.96363 0.00000
3 1 -0.499 0.412 -7.605 0.96363 0.00000
4 1 -0.499 0.412 -7.605 0.96363 0.00000
5 1 -0.499 0.412 -7.605 0.96363 0.00000
6 1 -0.499 0.412 -7.605 0.96363 0.00000
7 1 -0.499 0.412 -7.605 0.96363 0.00000
        :
        :

No. scan_no.

Frame serial number and scan serial number.

phix phiy phiz

Crystal orientation angles for the frame.

scaleF tempF

Frame scale factor and frame temperature factor.

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The resource.dat file is a basic information file. It contains the frame template, crystal data (including unit-cell parameters), wavelength, measurement box information, goniometer definition, refinement strategy, etc.

See here in detail.

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Spot position files are generated by the program fs_gen. The filename is normally "frame filename" + ".pos". The integration program fs_box3d and the display program graph read the file. If a folder named "POSFSQ" exists in the working folder, then spot position files are generated in the "POSFSQ" sub-folder.

A part of position file is shown below:

# cell: 5.15080 14.08590 14.94350 89.6590 89.9960 90.0129
# orientation: -a -b* -0.3790 0.2860 -7.4850
# h k l rcal scal wcal entry fail partial frame_num scan_num dr1 ds1 dw1 dr2 ds2 dw2 idom1 idom2 idn1 idn2 twin twov

-4 -5 -2 287.476 308.357 -120.177 0 0 0 1 1 68 14 -6 -68 -14 6 44 48 1 0 0 0
-4 -4 -2 277.158 322.936 -119.908 0 0 0 1 1 64 19 -6 -64 -19 6 45 49 0 1 0 0
-4 -3 -2 266.986 337.823 -119.893 0 0 0 1 1 61 24 -6 -61 -24 6 46 50 0 1 0 0
-4 -2 -2 256.878 353.144 -120.178 0 0 0 1 1 58 29 -6 -58 -29 6 48 52 1 0 0 0
-3 -6 -2 257.645 265.896 -119.689 0 0 0 1 1 57 1 -5 -57 -1 5 42 46 0 1 0 0
-3 -1 -2 205.632 339.177 -119.498 0 0 0 2 1 42 22 -4 -42 -22 4 48 51 1 1 0 0
-2 -5 -2 208.42 252.231 -120.222 0 0 0 1 1 42 -3 -3 -42 3 3 42 44 1 0 0 0
-2 -4 -2 197.717 266.553 -119.808 0 0 0 1 1 39 1 -3 -39 -1 3 41 44 0 1 0 0
          :

Line 1: comment line, showing cell parameters.
Line 2: comment line, showing crystal orientation angles.
  Note: even if crystallographic axes are converted by the program fs_axis, the Miller indices in the position files are not converted. To avoid confusion in such a case, the crystal orientation information is written.
Line 3: Column headings for the following items in the file.

File items:

h k l

Miller indices of a reflection.

rcal scal wcal

Spot position (X,Y,ω). X and Y are in pixel units; ω is in degrees.

entry

Entry/exit flag. Flag=2 indicates that the reflection is entering the Ewald sphere. Flag=0 indicates that it is exiting the sphere.

fail

If this flag is not equal to 0, the reflection is not suitable for integration.

partial

When generating observable reflections, the oscillation range is given. If a reflection cannot be integrated within this range, the partial flag is on. If, when evaluating integrated intensities, the option "-narrow" is given, the reflection is not integrated.

frame_num scan_num

Frame_num is the number of the frame at which the rocking curve top exists. Scan_num is the scan number.

dr1 ds1 dw1

Rcal, scal and wcal are the calculated spot positions using Kα radiation. These 3 values are differences in spot positions calculated by Kα1. The spot positions with Kα1 radiation are calculated by:

 Rcal1 = Rcal + dr1/100, Scal1 = Scal + ds1/100, Wcal1 = Wcal + dw1/100

dr2 ds2 dw2

Differences in spot positions just as (dr1 ds1 dw1) but with Kα2 radiation.

idom1 idom2

Width of the rocking curve. Let the width be [ω1,ω2], then

 ω1 = wcal - idom1/100, ω2 = wcal + idom2/100.

idn1 idn2

Width of the rocking curve expressed by frame number. Let the width be [#1,#2], then

 #1 = frame_num - idn1, #2 = frame_num + idn2.

twin twinov

For twin crystals: the twin flag indicates the domain number of the spot. Twinov is 1 when the spot is overlapped with another.

Back to file table

A spot intensity file, generated by fs_box3d, contains integrated intensities and observed spot positions. It is read by fs_lsq and fs_merge. When a sub-folder named "POSFSQ" exists, the spot file is saved in this sub-folder.

A part of *.fsq is shown below:

# cell: 5.15120 14.08380 14.94680 89.6630 89.9720 90.0056
# orientation: -a -b* -0.3620 0.2790 -7.4990
# lattice: P -1
# detector shift&set: -0.443 -0.291 0.886 0.336 -0.012 -0.288
# h k l fsq sig rawint entry robs sobs wobs frames status over under twin twov
-6 0 0 1078.04 90.7101 1334.45 0 326.617 456.126 -119.75 1 2 0 0 0 0
-5 -7 -1 6143.74 155.706 6532.13 0 351.489 307.345 -119.756 2 0 0 0 0 0
-5 0 -1 29226.2 175.056 45728 0 278.758 417.944 -119.679 2 0 0 0 0 0
-4 -12 0 -259.345 96.953 -258.519 0 366.848 200.855 -120.171 1 2 0 0 0 0
-4 -5 -2 611.768 78.355 893.912 0 283.038 307.285 -119.75 1 2 0 0 0 0
-4 -4 -2 2902.14 109.386 4504.86 0 276.525 323.111 -119.711 2 0 0 0 0 0
-4 -3 -2 1056.83 98.8955 1745.75 0 267.221 337.733 -119.564 2 0 0 0 0 0
-4 -2 -2 491.322 67.3228 865.702 0 254.257 353.517 -119.75 1 2 0 0 0 0
-4 5 0 5931.17 61.9102 20231.6 0 174.371 481.368 -119.73 2 2 0 0 0 0
-3 -14 1 924.516 134.256 999.133 0 350.964 135.235 -119.597 2 0 0 0 0 0
-3 -10 -1 15214.3 154.639 20703.7 0 300.177 205.923 -119.74 2 0 0 0 0 0
-3 -6 -2 4091.62 102.401 7125.23 0 257.596 265.905 -119.668 2 0 0 0 0 0
-3 -1 -2 60909 169.729 154469 0 205.63 339.289 -119.536 2 0 0 0 0 0
       :
       :

Line 1: comment line recording cell prarameters
Line 2: comment line recording crystal orientation
Line 3: comment line recording lattice centering and Laue class
Line 4: comment line recording detector shift vector and detector setting angles.
Line 5: Column headings for the following items in the file.

File items:

h k l

Miller indices.

fsq sig

LP-corrected intensity, observed F² and its standard error.

rawint

intensity, not LP-uncorrected .

entry

Entry/exit flag. Flag=0 indicates that the reflection is exiting the Ewald sphere; flag=2 indicates that it is entering the sphere.

robs sobs wobs

The observed spot position (X,Y,ω).

frames

Number of the frames over which the integrated intensity is evaluated.

status

A flag showing intensity measurement problems.

=0:

no problem,

=-1:

out of detectable area,

=1:

no backward frames for integration,

=2:

no forward frames for integration,

=3:

no backward or forward frames,

=4:

out of scan,

=5:

irregular background,

=6:

number of zero pixel intensities exceeds allowable number,

=7:

number of overloaded pixel intensities exceeds allowable number,

=8:

partial reflection

over under

number of zero-intensity pixels and number of overloaded-intensity pixels

twin twinov

For twin crystals: the twin flag indicates the domain number of the spot. Twinov is 1 when the spot is overlapped with another.

Back to file table

The program fs_merge collects all of the spot intensity files, sorts in order of Miller indices in an asymmetric unit, and outputs to the merge file. The name of the merge file is, by default, "word stem of frame files" + ".amer". The extension ".amer" means ASCII ('a') merge ("mer") file.

A part of the merge file is shown below:

# total: 6336
# space group: Pmmm
# absorption: abscor
# cell: 5.12985 14.05060 14.82700 90.0000 90.0000 90.0000
# frame range: 1 720
# h' k' l' fsq sig rawint h k l friedel entry robs sobs wobs frame nf status nover nunder absf oblique twin twov
0 0 1 0.39468 0.369131 13.9652 0 0 -1 2 0 68.9136 248.537 -105.329 390 3 0 0 0 0.943055 1 0 0
0 0 1 0.399625 0.391362 14.1378 0 0 1 2 2 46.0028 277.752 -100.498 399 3 0 0 0 0.947062 1 0 0
0 0 1 -1.0621 0.532359 -22.3039 0 0 1 2 2 33.9917 266.364 -2.38203 235 2 0 0 0 0.902194 1 0 0
0 0 1 0.846494 0.537331 17.7764 0 0 -1 2 0 79.6166 264.27 -5.46634 230 2 0 0 0 0.908485 1 0 0
0 0 2 6819.33 8.55553 71425.2 0 0 -2 2 0 98.0546 259.72 -6.75362 227 3 0 0 0 0.911897 1 0 0
0 0 2 6437.39 6.33272 113788 0 0 -2 2 0 81.6927 233.495 -107.709 385 3 0 0 0 0.93645 1 0 0
0 0 2 7085.36 6.67506 125198 0 0 2 2 2 29.7699 296.01 -98.2775 404 3 0 0 0 0.94396 1 0 0
0 0 3 36.1535 4.41512 251.402 0 0 -3 2 0 117.899 257.489 -8.22528 224 3 0 0 0 0.915263 1 0 0
0 0 3 19.4636 1.72362 229.013 0 0 -3 2 0 94.1694 218.572 -109.923 380 4 0 0 0 0.927214 1 0 0
0 0 4 541.527 3.66565 4768.76 0 0 -4 2 0 105.052 204.87 -112.302 376 3 0 0 0 0.915735 1 0 0
0 0 4 327.908 5.68723 1700.26 0 0 -4 2 0 136.102 255.881 -9.60539 221 2 0 0 0 0.91844 1 0 0
0 0 5 6.93076 5.23297 28.5369 0 0 -5 2 0 153.511 258.877 -10.6679 219 2 0 0 0 0.921311 1 0 0
     :

Line 1: Comment line showing number of reflections recorded in the file.
Line 2: Comment line showing space group symbol. Miller indices in an asymmetric unit are obtained using this space group.
Line 3: Comment line showing type of absorption correction, if applied.
Line 4: Comment line showing the unit cell dimensions.
Line 5: Comment line showing frame range of this file.
Line 6: Column headings for the following items in the file.

File items:

h' k' l'

Miller indices, transformed to the asymmetric unit.

DT> fsq sig

LP-corrected intensity and its standard error, F² and σ(F²)

DT>rawint

intensity, not LP-uncorrected.

h k l

original Miller indices

friedel

Friedel flag.

=1

F²(-)

=2

a reflection not distinguished as either F²(+) or F²(-)

=3

F²(+)

entry

Entry/exit flag. Flag=0 indicates that the reflection is exiting the Ewald sphere; flag=2 indicates that it is entering the sphere.

robs sobs wobs

The observed spot position (X,Y,ω).

frame

Frame number at which the maximum of the rocking curve exists.

nf

Number of frames over which intensity is integrated.

status

Only reflections with status=0 in the intensity files are saved in the merge file. If the status is not equal to 0, the reflection is marked as bad. The meanings of the various values for status are described in the intensity file (*.fsq) section.

nover nunder

Number of zero-intensity pixels and number of overloaded-intensity pixels.

absf

Absorption correction factor. Correction should be done by the equation:

     F²_corrected = F²_uncorrected / absf.

oblique

Oblique incidence correction factor.

twin twov

For twin crystals: the twin flag indicates the domain number of the spot. Twov is 1 when the spot is overlapped with another.

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The f2.dat file is in a space-delimited format. The intensities are scaled by frame scale factors, corrected by absorption factors, and averaged over symmetry-related reflections. (This file name can be used in teXsan or CrystalStructure to input generic diffractometer data.)

A sample of the file is given below:

 0   0   1 0.248833 0.308659
 0   0   2 7037.87 54.5099
 0   0   3 21.9428 2.70672
 0   0   4 513.696 11.3003
 0   0   5 0.880426 3.51227
 0   0   6 26660.3 407.173
 0   0   7 -1.17853 4.64527
 0   0   8 16236.8 286.934
 0   0   9 7.35281 5.66481
 0   0  10 33.5431 7.50546
 0   0  11 -2.12018 6.34741
 0   0  12 117.97 13.5381
            :
            :

Format: h k l FSQ SIG

h k l:

Miller indices, transformed to the asymmetric unit.

FSQ SIG:

Averaged F² and σ(²).

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A standard reflection input file for teXsan or CrystalClear. Intensities are LP-corrected and frame scaled but not averaged. The intensity is not absorption-corrected but the correction factor is given as the seventh value in each record.

A part of the file is given below:

 0   0  -1 0.385916 0.509951 13.9652 0.943055 1
 0   0   1 0.375987 0.520235 14.1378 0.947062 1
 0   0   1 -1.1554 0.818223 -22.3039 0.902194 1
 0   0  -1 0.922016 0.826908 17.7764 0.908485 1
 0   0  -2 6294.44 74.8725 113788 0.93645 1
 0   0   2 6980.17 79.514 125198 0.94396 1
 0   0  -3 39.379 8.53477 251.402 0.915263 1
 0   0  -3 18.1597 2.85406 229.013 0.927214 1
 0   0  -4 505.25 12.9082 4768.76 0.915735 1
 0   0  -4 357.163 23.38 1700.26 0.91844 1
 0   0  -5 7.28212 7.95336 28.5369 0.921311 1
 0   0  -5 -0.741042 3.91467 -5.5808 0.902442 1
 0   0  -6 25378.6 715.22 82129.9 0.923784 1
 0   0  -6 23322.9 495.265 146528 0.887787 1
 0   0  -7 -8.17508 12.2931 -22.436 0.925793 1

Format: h k l fsq sig rawint absf decayf

h k l

Miller indices.

fsq sig

Scaled, LP-corrected, and absorption uncorrected F² and its standard error. Individual intensities not averaged.

rawint

Raw intensity without LP correction.

absf

absorption correction factor.

decayf

crystal decay factor but always 1.

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d*TREK reflection file. Intensities are scaled, LP-corrected, absorption corrected, and averaged.

Top part of the file:

3 2 0 5
CRYSTAL_DESCRIPTION=unknown;
CRYSTAL_MOSAICITY=0.634;
CRYSTAL_ORIENT_ANGLES=0.0 0.0 0.0;
CRYSTAL_SPACEGROUP=unknown;
CRYSTAL_UNIT_CELL=5.1298 14.0506 14.8270 90.0000 90.0000 90.0000;
nH
nK
nL
fIntensity
fSigmaI
    0    0    1 0.249 0.309
    0    0    2 7037.867 54.510
    0    0    3 21.943 2.707
    0    0    4 513.696 11.300
    0    0    5 0.880 3.512
    0    0    6 26660.273 407.173
    0    0    7 -1.179 4.645
    0    0    8 16236.773 286.934
    0    0    9 7.353 5.665
    0    0   10 33.543 7.505

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SHELX-formatted reflection data (HKLF4 type).

   0   0  -1    0.00    0.01
   0   0   1    0.00    0.01
   0   0   1   -0.01    0.01
   0   0  -1    0.01    0.01
   0   0  -2   67.22    0.80
   0   0   2   73.95    0.84
   0   0  -3    0.43    0.09
   0   0  -3    0.20    0.03
   0   0  -4    5.52    0.14
   0   0  -4    3.89    0.25
   0   0  -5    0.08    0.09
   0   0  -5   -0.01    0.04
   0   0  -6  274.72    7.74
   0   0  -6  262.71    5.58

Format: h k l fsq sig

h k l

Miller indices

fsq sig

Scaled, LP-corrected, absorption-corrected individual intensities and standard error.

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The texray.inf file is created by fs_final when the sample type is small-molecule. This information file is used to pass crystal, data, and experimental parameters to the teXsan or CrystalStructure programs. See the teXsan or CrystalStructure manuals for details.

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Record 1: scan_num, nref, max3d, max2d, box_size

Record 2: h, k, l, entry, fail, partial, rcal, scal, wcal, robs, sobs, wobs, rcal1, scal1, wcal1, rcal2, scal2, wcal2, fw1, fw2, dom1, dom2, fsq_sheet[10], x1, y1, z1, x2, y2, z2, z1m, z2m, nf, dum, n1d, n2d, n3d, status, nover, nunder

Record 3: Pixel intensities. Size of this record is short * max3d, but substantially occupied are short * n3d.

Record 4 and after: Repeat of record 2-3 by nref times.

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A definition of the blind areas on the detector to be ignored during integration.

An example of a blind.dat file:

10 1195 2554 1195 2554 1380 1304 1443 1329 1274 2557 
-1 1415 1258 116

Format1: n x1 y1 x2 y2 ... x(n/2) y(n/2)

Format2: -1 x y r

n

For a polygon, the number of data on this line in the file.

x(n) y(n)

For a polygon, the pixel coordinates for each apex. The minimum number of coordinates is 3. A line is drawn between each successive pair of coordinates, and a line is drawn between the first and last pair. If any part of an integration box lies within the polygon, the reflection is rejected.

-1 x y r

If the first entry on a line is -1, then that line defines a circle with center at pixel coordinates x,y and radius of r pixels.

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