Examples

standard run

Standard run

eval14 started on schol at 19-Apr-2002 13:40:21
Version:22 Nov 2001

Appending eval14.log
Enter *.shoe* filename [s14f001.shoe]

You enter the name of the boxfile (the default is the last modified .shoe file in the current directory) or the sequence number of the boxfile. In this case we answer 2.

Enter *.shoe* filename [s14f001.shoe] 2
filename set to s01f002.shoe
Trying xtal.evc
!! Spheric xtal dia 0.3 (mm)
!! Isotropic Mosaicity 0.3 (degrees)
!! Collimator 1.0
!! Focus 220.0 0.4 0.4
!! chi 65.0
!! 10 shifts allowed
!! Maximum shifts: hor 3.0 ver 3.0 (mm) rot 3.0 (degrees) xy 4.24 mm
!! ShiftInit hor 0.0 ver 0.0 (mm) rot 0.0 (degrees)
!! DxFactor 1.0
!! ExpandMargin 1.0 (pixels) ExpandDepth 1.5 (images)
!! noautoexpand
!! Remove pixels 3.0*sigma off plane
!! PQOBSERVED 20
!! BADBG 1.0 bad background if BgQual is greater
!! flag badbg if I/Sig > 2.5
!! allow shifts if I/Sig > 2.5
!! shiftshare 0.2 shift if Nshare/(Npeak+Nshare)<shiftshare
!! sumfactor 0.7 sum if Nshare/(Npeak+Nshare)>sumfactor
!! splitpqratio 1000.0 split if PQHigh/PQlow > splitpqratio
!! splitfactor 0.1 split if Nshare/(Npeak+Nshare)<splitfactor
change any of these data [Yes]

Here you see the default parameters. Lets set the crystal size to 0.2mm and the mosaic spread to 0.2° All the other values are ok (for now), so we may answer all to select the remaining defaults.

change any of these data [Yes] Yes
Spherical Crystal [yes]
Sphere dia (mm)[0.3] 0.2
Isotropic mosaicity[0.3] 0.2
Extra Anisotropic Mosaicity [no] all
!! Spheric xtal dia 0.2 (mm)
!! Isotropic Mosaicity 0.2 (degrees)
!! Collimator 1.0
!! Focus 220.0 0.4 0.4
!! chi 65.0
!! 10 shifts allowed
!! Maximum shifts: hor 3.0 ver 3.0 (mm) rot 3.0 (degrees) xy 4.24 mm
!! ShiftInit hor 0.0 ver 0.0 (mm) rot 0.0 (degrees)
!! DxFactor 1.0
!! ExpandMargin 1.0 (pixels) ExpandDepth 1.5 (images)
!! noautoexpand
!! Remove pixels 3.0*sigma off plane
!! PQOBSERVED 20
!! BADBG 1.0 bad background if BgQual is greater
!! flag badbg if I/Sig > 2.5
!! allow shifts if I/Sig > 2.5
!! shiftshare 0.2 shift if Nshare/(Npeak+Nshare)<shiftshare
!! sumfactor 0.7 sum if Nshare/(Npeak+Nshare)>sumfactor
!! splitpqratio 1000.0 split if PQHigh/PQlow > splitpqratio
!! splitfactor 0.1 split if Nshare/(Npeak+Nshare)<splitfactor
save data in xtal.evc [Yes]

It is wise to save the parameters in the file xtal.evc. In a next run, this file is automatically read in.

save data in xtal.evc [Yes] Yes
Created xtal.evc
s01f002.shoe Opened
Trying s01f002.evc
Refl nr [1]

So now we may select a reflection. Select the proposed one.

KappaSupport 50.001469 IncidenceCoefficient 0.342
Omega 160.0 Kappa 0.0 Phi 0.0
ToGoniostatMat
  -0.9396926   0.3420202   0.0000000
  -0.3420202  -0.9396926   0.0000000 Determinant:  1.000000
   0.0000000   0.0000000   1.0000000
SCAN PHI PIXELSIZE 0.11 0.11 DETECTORSIZE 34.375 31.68
Dist 40.0 Swing -15.61 GAIN 1.62
Cell 4.7686 6.0022 10.2446 89.989 90.004 89.997 Volume 293.2
Alpha1 0.7093 Alpha2 0.71359 AlphaRatio 2.0 Mid 0.711445 Mean 0.71073
thetamonochr 5.98 polar 0.489028
Neighbour check ON
            RMAT000[1]                              at Goniostat
   0.1003128  -0.0944744  -0.0654408       -0.1469302   0.0979245   0.0394718
  -0.1539881   0.0267458  -0.0643894        0.1103925   0.0071793   0.0828883
   0.1009972   0.1345967  -0.0331619        0.1009972   0.1345967  -0.0331619
Determinant:  0.3410335E-02                            0.3410335E-02
timescale minutes/degree

The graphics window pops up.

First we see some of the parameters from the boxfile header.

The scan axis is PHI.
Note the goniostat position: Omega 160.0 Kappa 0.0 Phi 0.0. Phi is set to zero, because the actual phi values will be given later for each reflection.
ToGoniostatMat is the transformation matrix to change from goniostat with all angles zero to the goniostat position.
mid is the average wavelength 0.5*(alpha1+alpha2), mean is the weighted average: (alpharatio*alpha1+alpha2)/(alpharatio+1)
Neighbour check ON. eval14 will use neighbour reflections.
RMAT000 is the rmatrix at zero position.
timescale is used to correct for different exposuretimes and/or rotation increments.

And then we get the results for the first reflection:

Orig: hor=13.65 ver=7.2 rot=69.87 hkl: 13.68 7.21 69.89 diff: -0.03 -0.01 -0.02
Frame: 6.7 6.51 6.53 6.04 6.12
Theta:17.83 Chi:15.93
Contour: H(13.33,14.12)=0.79[7] V(6.82,7.58)=0.76[7] R(-1.28,0.72)=2.0[2]
Pixels: Peak=80/3.6% Surface=126 Bg=2118
Excluded: 7 I(Ex/Pk)=1.03% BadI 0.04%
Background: A=-0.01 B=0.0 C=6.41 Sig=1.79 Slope=0.11
Intensity: Hor=558.33 Ver=569.04 Rot=586.83 Plane=580.09 BgQual=0.05 peakbg=580.31
Shifts:2 H 0.4px 0.04mm V -0.04px 0.0mm rot=0.14 dxfactor=1.00141 GravRot 2.74
Final Impact: 13.73 7.2 70.03
Rnet=580.09 Poisson=33.31 GarbageSigma=0.23 Weight=15.99 PQ=36 I/Sig=17.42
Corrections: Lorentz:1.2726 Polar:0.8265 LP:0.9507 Incidence:0.9778 Speed:3.0 Final:2.7889
Corrected: Rnet=1617.79 Sigma=92.89
   nr   h   k   l QVP   DetH   DetV     Rot         Int sigPois   PQ obxXyYzZ
    1   4  -1   1      13.73   7.20   70.03      1617.8    92.9   36 ........
Refl nr [2]

Orig: hor=13.65 ver=7.2 rot=69.87 hkl: 13.68 7.21 69.89 diff: -0.03 -0.01 -0.02
First the impact position and rotation angle as found in the boxfile. Second the impact position and rotation angle as calculated from rmatrix, goniostat- and detector position. And finally the differences between those numbers. These differences should be zero or small. Small differences are caused by rounding errors.
Frame: 6.7 6.51 6.53 6.04 6.12
The average intensity in the background pixels for each frame. These numbers are not used (yet). If they differ a lot, the handling of the background could go wrong.
Theta:17.83 Chi:15.93
The values of theta and chi are printed.
Contour: H(13.33,14.12)=0.79[7] V(6.82,7.58)=0.76[7] R(-1.28,0.72)=2.0[2]
Some numbers on the eval14 contours.
- Horizontal: contour from 13.33 to 14.12 mm. Contour width 0.79 mm = 7 pixels.
- Vertical: contour from 6.82 to 7.58 mm. Contour height 0.76 mm = 7 pixels.
- Rotation: contour from -1.28 to 0.72. Contour width 2° = 2 frames. Note the rotation values are always brought back to something around zero.
Pixels: Peak=80/3.6% Surface=126 Bg=2118
There are 80 pixels within the peak (3.6% of all the pixels). 126 pixels lie on the surface of the peak. And 2118 pixels are in the background.
Excluded: 7 I(Ex/Pk)=1.03% BadI 0.04%
7 pixels are excluded from the background (badbg pixels, coloured blue in the bottom row).
Iex=Intensity of the excluded pixels; Ipk=Intensity of the peak. So the excluded intensity is only 1% of the peak intensity.
If pixels are excluded from the background, there is always a chance that there should be excluded pixels within the peak (you would see those pixels if the intensity of the peak is zero). BadI is an estimate of the relative intensity of those pixels. (see ExcludedSigma in the Integration page.
Background: A=-0.01 B=0.0 C=6.41 Sig=1.79 Slope=0.11
The background plane parameters.

P = A*hor + B*ver + C.
Sig is the sigma of the least squares plane.
Calculate the background plane values for each of the four corners of the box Hor-Ver projection. Slope is defined as

(max-min)/sigma.
Intensity: Hor=558.33 Ver=569.04 Rot=586.83 Plane=580.09 BgQual=0.05 peakbg=580.31
Hor, Ver and Rot are BPB net intensities in the 3 directions. Plane is the result from the background plane subtraction (see plane). The background quality (BgQual) is also described in BPB paragraph. A BGQual of zero is high quality. If BGQUAL>badbg the reflection will be flagged B.
The intensity of Plane will be used for the final intensity.
Shifts:2 H 0.4px 0.04mm V -0.04px 0.0mm rot=0.14 dxfactor=1.00141 GravRot 2.74
2 shifts were carried out. Horizontal: 0.4 pixel of 0.04 mm. Vertical -0.04 pixel or 0.0 mm. Rotation: 0.14° DXfactor for this reflection after shift is 1.00141. Gravrot is the centre of gravity of the final peak position in the rotation direction.
Final Impact: 13.73 7.2 70.03
The impact position after shifts.

Rnet=580.09 Poisson=33.31 Excluded=0.23 Weight=15.99 PQ=36 I/Sig=17.42

Name	Integration Page Paragraph	Description
Rnet	plane	Final Intensity
Poisson	Sigma Poisson	estimate of the sigma
Excluded	Sigma Excluded	estimate of the contribution of bad pixels
Weight	Peak Quality
PQ	Peak Quality	Peak Quality
I/Sig		Rnet divided by Poisson

The largest of Sigma Poisson and Sigma Excluded will be used

Corrections: Lorentz:1.2726 Polar:0.8265 LP:0.9507 Incidence:0.9778 Speed:3.0 Final:2.7889
There are four corrections applied to the final intensity: Lorentz multiplied by Polar (the lorentz and polarisation corrections) result in LP. Incidence is a correction for the incidence angle. Speed is used to scale the intensities to the same experimental speed (so the resulting intensity is independent of rotation increment and integration time). All these corrections result into one factor, called Final.
Corrected: Rnet=1617.79 Sigma=92.89
Rnet is now the net intensity (580.09) multiplied with the final scale (2.7889) Sigma is Poisson multiplied by the same factor.

Eval14