************ Version 7.0.0 (beta test) for Image plate and CCD data 14th June 2006 ***********
A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
E-mail andrew@mrc-lmb.cam.ac.uk
New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
(1998) J. Appl. Cryst. 30, 1036-1040
Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
(Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
===> newmat autoindex.mat
===> directory /scisoft/users/svensson/tmp/srpol-HA00AG3240_1
===> template ref-srpol-HA00AG3240_1_###.img
===> BEST ON
===> prerefine on
****** Keyword NOT RECOGNISED *****
===> autoindex dps refine image 1 thresh 10.000000
Using DPS code for background indexing
Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution
===> autoindex dps refine image 2 thresh 10.000000
Using DPS code for background indexing
Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution
===> mosaic estimate
===> go
From information in the image file, the detector has been
recognized as: ADSC
If this is incorrect you must supply a DETECTOR keyword
Crystal to detector distance of 278.71mm taken from image header
Wavelength of 1.00500A taken from image header
Pixel size of 0.1026mm taken from image header.
Start and end phi values for image 0 from image header are 0.00 and 0.50 degrees.
Oscillation axis set as PHI from image header
Main beam position has been calculated as 156.94mm 158.85mm from parameters
in the image header. You should check these values carefully as they may
be in error!
Autoindexing using 2 images
Image numbers: 1 2
image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_001.img
Determining average spot size for spots in centre of image.
==========================================================
Determining best threshold for spot finding.
Default parameters may be reset with SPOTS keyword.
Minimum radius 15.8mm, maximum radius 63.07mm, minimum number of spots 10
Threshold set to 5.0
Threshold set to 5.0
Based on a median spot size of 3 by 3 pixels in X and Y, the measurement box
parameters have been set to 13 13 8 4 4
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 3 by 3 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.51 0.51mm.
Closest possible spot separation is 0.00mm.
Determining best threshold for spot finding.
Default parameters may be reset with SPOTS keyword.
Minimum radius 15.8mm, maximum radius 63.07mm, minimum number of spots 10
Threshold set to 5.0
Threshold set to 5.0
Finding spots on image 1 (Midpoint of phi 0.250 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 0.0mm from the image centre in Y to avoid any
backstop shadow
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.81mm
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.91mm
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.01mm
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.11mm
Radial Background calculation complete
RADIUS 15.7 16.1 16.5 16.9 17.3 17.7 18.2 18.6 19.0 19.4 19.8 20.2
BACKG 46 46 45 44 44 45 45 44 42 45 45 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 0 1 9 12 7 3 1 13 16 4 5 3
RADIUS 20.6 21.0 21.4 21.9 22.3 22.7 23.1 23.5 23.9 24.3 24.7 25.1
BACKG 45 43 43 45 45 44 45 44 43 44 46 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 5 13 12 5 3 6 4 12 16 6 1 6
RADIUS 25.5 26.0 26.4 26.8 27.2 27.6 28.0 28.4 28.8 29.2 29.6 30.1
BACKG 44 43 44 45 45 46 45 45 45 45 45 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 9 14 8 4 3 2 6 15 6 3 4 7
RADIUS 30.5 30.9 31.3 31.7 32.1 32.5 32.9 33.3 33.8 34.2 34.6 35.0
BACKG 46 44 44 45 45 45 44 44 44 45 45 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 3 12 9 5 6 4 9 11 15 6 6 10
RADIUS 35.4 35.8 36.2 36.6 37.0 37.4 37.9 38.3 38.7 39.1 39.5 39.9
BACKG 45 44 43 45 45 45 45 44 44 44 43 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 4 11 14 9 4 4 1 7 15 15 17 11
RADIUS 40.3 40.7 41.1 41.5 42.0 42.4 42.8 43.2 43.6 44.0 44.4 44.8
BACKG 45 46 46 44 44 44 45 44 44 45 45 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 6 3 7 11 10 11 7 11 7 6 5 5
RADIUS 45.2 45.7 46.1 46.5 46.9 47.3 47.7 48.1 48.5 48.9 49.3 49.8
BACKG 43 44 44 45 45 46 45 46 46 44 46 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 15 9 14 8 5 2 2 2 3 16 7 6
RADIUS 50.2 50.6 51.0 51.4 51.8 52.2 52.6 53.0 53.4 53.9 54.3 54.7
BACKG 45 45 44 43 37 42 42 44 45 45 45 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 9 7 9 20 51 25 29 16 9 9 8 6
RADIUS 55.1 55.5 55.9 56.3 56.7 57.1 57.6 58.0 58.4 58.8 59.2 59.6
BACKG 45 45 45 45 45 44 44 46 43 44 43 46
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 7 5 4 3 8 14 15 4 21 23 27 10
RADIUS 60.0 60.4 60.8 61.2 61.7 62.1 62.5 62.9 63.3 63.7 64.1 64.5
BACKG 45 46 46 47 48 48 49 48 48 48 49 47
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 11 10 11 2 2 6 3 3 11 9 5 16
RADIUS 64.9 65.3 65.8 66.2 66.6 67.0 67.4 67.8 68.2 68.6 69.0 69.5
BACKG 48 49 50 50 51 50 50 50 50 49 49 49
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 12 7 7 6 3 2 5 4 4 12 13 12
RADIUS 69.9 70.3 70.7 71.1 71.5 71.9 72.3 72.7 73.1 73.6 74.0 74.4
BACKG 49 51 51 51 51 51 52 51 50 52 53 52
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 15 5 7 5 3 8 11 10 17 12 9 14
RADIUS 74.8 75.2 75.6 76.0 76.4 76.8 77.2 77.7 78.1 78.5 78.9 79.3
BACKG 53 55 54 54 55 53 55 54 56 56 56 56
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 8 6 7 11 10 18 9 11 9 10 11 10
RADIUS 79.7 80.1 80.5 80.9 81.4 81.8 82.2 82.6 83.0 83.4 83.8 84.2
BACKG 55 55 56 56 57 56 54 53 54 55 54 55
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 16 11 9 7 4 12 10 16 15 5 9 9
RADIUS 84.6 85.0 85.5 85.9 86.3 86.7 87.1 87.5 87.9 88.3 88.7 89.1
BACKG 55 54 54 54 54 55 53 52 52 52 54 52
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 10 8 9 11 8 5 11 13 14 9 5 7
RADIUS 89.6 90.0 90.4 90.8 91.2 91.6 92.0 92.4 92.8 93.3 93.7 94.1
BACKG 52 52 50 51 51 52 51 51 50 51 50 50
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 12 10 16 4 8 7 8 6 9 3 6 9
RADIUS 94.5 94.9 95.3 95.7 96.1 96.5 96.9 97.4 97.8 98.2 98.6 99.0
BACKG 50 50 48 49 48 49 49 48 49 48 48 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 7 7 8 4 6 7 6 5 7 4 4 13
RADIUS 99.4 99.8 100.2 100.6 101.0 101.5 101.9 102.3 102.7 103.1 103.5 103.9
BACKG 47 47 46 47 45 46 46 46 45 44 45 47
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 8 4 15 6 17 8 6 4 11 16 10 5
RADIUS 104.3 104.7 105.2 105.6 106.0 106.4 106.8 107.2 107.6 108.0 108.4 108.8
BACKG 45 46 46 46 46 45 45 45 45 46 46 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 13 7 4 4 4 8 10 8 5 4 4 3
RADIUS 109.3 109.7 110.1 110.5 110.9 111.3 111.7 112.1 112.5 112.9 113.4 113.8
BACKG 45 46 44 45 44 45 44 45 44 44 46 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 6 4 11 7 4 2 13 7 13 8 1 7
RADIUS 114.2 114.6 115.0 115.4 115.8 116.2 116.6 117.1 117.5 117.9 118.3 118.7
BACKG 45 44 45 44 44 44 44 44 45 44 43 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 5 5 7 9 10 5 12 5 3 11 13 5
RADIUS 119.1 119.5 119.9 120.3 120.7 121.2 121.6 122.0 122.4 122.8 123.2 123.6
BACKG 45 44 43 44 43 45 45 45 45 44 44 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 3 5 10 10 9 3 2 5 8 9 8 8
RADIUS 124.0 124.4 124.8 125.3 125.7 126.1 126.5 126.9 127.3 127.7 128.1 128.5
BACKG 45 44 44 44 44 45 44 44 44 45 45 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 6 7 6 14 10 6 7 7 8 6 7 5
RADIUS 129.0 129.4 129.8 130.2 130.6 131.0 131.4 131.8 132.2 132.6 133.1 133.5
BACKG 44 44 45 44 44 44 44 45 45 44 44 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 10 8 2 8 6 13 12 10 7 7 9 8
RADIUS 133.9 134.3 134.7 135.1 135.5 135.9 136.3 136.7 137.2 137.6 138.0 138.4
BACKG 46 46 45 44 45 45 45 45 45 46 44 45
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 3 3 3 8 3 6 5 6 4 3 7 6
RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7
BACKG 44 46 46 45 45 45 45 11
SIGMA 3 3 3 3 3 3 3 2
NREJ 12 6 3 7 7 6 6 1
Starting spot search...
Number of spots excluded from possible ice rings: 91
Median spot size is 8 x 6 pixels, mode size is 6 by 6
Total number of spots found: 594
Number rejected as too small on X: 67
Number rejected as too small on Y: 4
Number rejected as too big on X: 34
Number rejected as too big on Y: 10
Number too close (SEPARATION keyword): 33
(currently SEPARATION 0.51 0.51)
Number stored as OK: 374
highest resolution is 2.16 Angstrom
99% have resolution less than 3.48 Angstrom
Number of spots found in each bin
9 8 8 14 22 15 13 22
33 25 33 28 35 43 33 70
0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_002.img
Finding spots on image 2 (Midpoint of phi 89.750 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 0.0mm from the image centre in Y to avoid any
backstop shadow
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.81mm
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.91mm
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.01mm
** WARNING **
Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.11mm
Radial Background calculation complete
RADIUS 15.7 16.1 16.5 16.9 17.3 17.7 18.2 18.6 19.0 19.4 19.8 20.2
BACKG 44 44 44 42 43 44 43 44 43 43 44 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 2 4 8 13 5 5 9 7 11 11 5 5
RADIUS 20.6 21.0 21.4 21.9 22.3 22.7 23.1 23.5 23.9 24.3 24.7 25.1
BACKG 43 43 42 43 43 44 43 42 43 43 45 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 8 10 16 7 6 4 6 11 12 7 7 7
RADIUS 25.5 26.0 26.4 26.8 27.2 27.6 28.0 28.4 28.8 29.2 29.6 30.1
BACKG 43 42 43 44 44 43 43 43 45 43 43 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 10 16 7 2 4 7 12 15 10 20 10 7
RADIUS 30.5 30.9 31.3 31.7 32.1 32.5 32.9 33.3 33.8 34.2 34.6 35.0
BACKG 44 42 43 43 43 44 43 43 44 43 44 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 13 13 8 5 3 6 8 9 11 11 3 2
RADIUS 35.4 35.8 36.2 36.6 37.0 37.4 37.9 38.3 38.7 39.1 39.5 39.9
BACKG 43 43 42 42 43 43 43 43 43 42 42 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 6 10 15 13 7 9 5 10 12 11 15 11
RADIUS 40.3 40.7 41.1 41.5 42.0 42.4 42.8 43.2 43.6 44.0 44.4 44.8
BACKG 43 43 43 43 42 43 42 44 44 44 44 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 7 4 7 7 14 13 14 8 5 4 4 10
RADIUS 45.2 45.7 46.1 46.5 46.9 47.3 47.7 48.1 48.5 48.9 49.3 49.8
BACKG 44 41 43 43 43 43 44 43 43 43 43 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 7 21 9 12 6 7 3 7 6 13 13 9
RADIUS 50.2 50.6 51.0 51.4 51.8 52.2 52.6 53.0 53.4 53.9 54.3 54.7
BACKG 44 42 43 40 34 41 43 42 41 43 42 43
SIGMA 3 3 3 3 2 3 3 3 3 3 3 3
NREJ 9 13 9 22 51 18 14 15 16 9 8 7
RADIUS 55.1 55.5 55.9 56.3 56.7 57.1 57.6 58.0 58.4 58.8 59.2 59.6
BACKG 43 42 42 43 43 42 43 42 42 42 41 42
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 9 9 11 11 10 9 7 11 16 18 22 18
RADIUS 60.0 60.4 60.8 61.2 61.7 62.1 62.5 62.9 63.3 63.7 64.1 64.5
BACKG 41 42 43 42 44 44 44 44 43 44 44 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 17 16 10 16 6 7 14 11 10 10 10 16
RADIUS 64.9 65.3 65.8 66.2 66.6 67.0 67.4 67.8 68.2 68.6 69.0 69.5
BACKG 43 44 44 44 46 44 45 45 45 45 44 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 16 11 6 9 5 12 4 10 8 15 19 19
RADIUS 69.9 70.3 70.7 71.1 71.5 71.9 72.3 72.7 73.1 73.6 74.0 74.4
BACKG 45 46 45 46 48 47 47 44 46 46 47 48
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 16 6 11 4 0 5 4 16 9 14 4 4
RADIUS 74.8 75.2 75.6 76.0 76.4 76.8 77.2 77.7 78.1 78.5 78.9 79.3
BACKG 48 49 48 48 48 47 49 48 49 49 49 48
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 2 2 6 8 10 13 9 8 3 4 6 10
RADIUS 79.7 80.1 80.5 80.9 81.4 81.8 82.2 82.6 83.0 83.4 83.8 84.2
BACKG 49 48 49 49 49 50 50 48 49 50 48 49
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 9 6 5 2 3 5 7 9 10 5 10 5
RADIUS 84.6 85.0 85.5 85.9 86.3 86.7 87.1 87.5 87.9 88.3 88.7 89.1
BACKG 49 49 49 49 48 48 48 48 48 49 48 48
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 8 7 10 6 6 5 10 7 7 5 5 4
RADIUS 89.6 90.0 90.4 90.8 91.2 91.6 92.0 92.4 92.8 93.3 93.7 94.1
BACKG 47 47 47 47 47 47 47 46 46 46 45 46
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 10 13 9 8 4 5 5 17 2 4 8 10
RADIUS 94.5 94.9 95.3 95.7 96.1 96.5 96.9 97.4 97.8 98.2 98.6 99.0
BACKG 45 44 43 46 44 44 45 43 45 43 44 44
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 12 17 17 10 11 16 8 15 4 16 14 11
RADIUS 99.4 99.8 100.2 100.6 101.0 101.5 101.9 102.3 102.7 103.1 103.5 103.9
BACKG 44 44 44 43 43 44 42 44 43 42 42 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 11 6 6 9 13 8 16 6 11 13 15 9
RADIUS 104.3 104.7 105.2 105.6 106.0 106.4 106.8 107.2 107.6 108.0 108.4 108.8
BACKG 43 43 42 43 43 43 43 42 43 43 43 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 12 6 13 11 5 6 13 12 11 7 8 11
RADIUS 109.3 109.7 110.1 110.5 110.9 111.3 111.7 112.1 112.5 112.9 113.4 113.8
BACKG 42 43 41 42 42 42 43 42 42 42 43 41
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 8 6 12 7 8 7 8 4 9 11 5 10
RADIUS 114.2 114.6 115.0 115.4 115.8 116.2 116.6 117.1 117.5 117.9 118.3 118.7
BACKG 42 42 42 43 42 42 42 42 42 41 42 41
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 9 6 10 5 7 9 10 7 5 11 8 16
RADIUS 119.1 119.5 119.9 120.3 120.7 121.2 121.6 122.0 122.4 122.8 123.2 123.6
BACKG 42 41 41 41 42 42 41 41 42 41 42 41
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 7 12 13 12 6 8 12 10 6 9 9 9
RADIUS 124.0 124.4 124.8 125.3 125.7 126.1 126.5 126.9 127.3 127.7 128.1 128.5
BACKG 41 42 42 42 41 42 42 42 41 42 41 42
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 13 9 8 10 14 8 9 11 10 10 8 12
RADIUS 129.0 129.4 129.8 130.2 130.6 131.0 131.4 131.8 132.2 132.6 133.1 133.5
BACKG 42 42 42 41 41 42 41 42 42 42 42 41
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 11 10 7 9 9 12 12 5 6 11 8 15
RADIUS 133.9 134.3 134.7 135.1 135.5 135.9 136.3 136.7 137.2 137.6 138.0 138.4
BACKG 43 41 42 42 42 41 42 42 42 42 42 43
SIGMA 3 3 3 3 3 3 3 3 3 3 3 3
NREJ 5 9 8 9 10 9 8 8 8 8 7 5
RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7
BACKG 41 42 41 42 42 42 41 10
SIGMA 3 3 3 3 3 3 3 2
NREJ 12 8 10 8 8 10 12 3
Starting spot search...
Number of spots excluded from possible ice rings: 45
Median spot size is 6 x 5 pixels, mode size is 4 by 3
Total number of spots found: 281
Number rejected as too small on X: 11
Number rejected as too small on Y: 12
Number rejected as too big on X: 17
Number rejected as too big on Y: 1
Number too close (SEPARATION keyword): 8
(currently SEPARATION 0.51 0.51)
Number stored as OK: 215
highest resolution is 2.19 Angstrom
99% have resolution less than 3.74 Angstrom
Number of spots found in each bin
9 4 7 9 4 6 5 10
5 9 5 7 14 10 10 8
3 4 3 10 16 7 6 15
3 2 8 3 6 4 2 5
0 0 0 0 0 1 1 0
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-srpol-HA00AG3240_1.spt, Filename: ref-srpol-HA00AG3240_1.spt
374 spots written for image 1
215 spots written for image 2
A total of 589 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-srpol-HA00AG3240_1.spt, Filename: ref-srpol-HA00AG3240_1.spt
DPS Indexing using 101 reflections with I >= 10 I/sigma(I)
DPS Indexing at Two-theta = 0.00 with 101 reflections (minimum spot separation = 0.51mm. Maximum expected cell edge 277.33, Beam position is 156.94 158.85
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 3
CELL(start) = 170.625 199.192 200.316 117.20 100.45 79.23
CELL(finis) = 171.063 200.199 200.372 117.17 100.36 79.63
Using 89 out of 101 reflections
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
44 999 unrefined cI 269.93 238.76 200.37 75.3 73.2 88.8 I23,I213,I432,I4132
43 830 unrefined tI 208.80 348.51 171.06 73.5 90.0 90.1 I4,I41,I422,I4122
42 829 unrefined oF 171.06 406.09 406.44 61.9 104.1 104.1 F222
41 643 unrefined hR 348.51 356.94 171.06 84.2 73.5 114.9 H3,H32 (hexagonal settings of R3 and R32)
238.76 200.37 208.80 121.5 121.3 106.9 R3,R32 (primitive rhombohedral cell)
40 572 unrefined hR 285.79 238.92 269.92 88.9 100.2 99.2 H3,H32 (hexagonal settings of R3 and R32)
200.20 171.06 200.37 79.6 122.3 100.4 R3,R32 (primitive rhombohedral cell)
39 565 unrefined tI 200.37 269.93 238.76 88.8 75.3 73.2 I4,I41,I422,I4122
38 564 unrefined hP 171.06 200.20 208.80 121.4 90.0 100.4 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
37 555 unrefined cF 269.92 269.93 348.51 100.4 100.3 101.3 F23,F432,F4132
36 554 unrefined hR 171.06 238.76 544.17 78.6 100.5 124.4 H3,H32 (hexagonal settings of R3 and R32)
200.37 238.92 208.80 64.0 64.0 47.1 R3,R32 (primitive rhombohedral cell)
35 527 unrefined oF 238.76 285.79 379.93 72.5 98.5 80.9 F222
34 505 unrefined tI 171.06 200.20 379.93 82.7 69.2 79.6 I4,I41,I422,I4122
33 505 unrefined mC 171.06 406.44 200.20 68.0 100.4 75.9 C2
32 505 unrefined mC 171.06 406.09 200.37 68.0 100.4 75.9 C2
31 487 unrefined cP 171.06 200.20 208.80 121.4 90.0 100.4 P23,P213,P432,P4232,P4332,P4132
30 449 unrefined tP 171.06 200.20 208.80 121.4 90.0 100.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
29 449 unrefined oC 171.06 406.09 208.80 59.1 90.0 104.1 C222,C2221
28 449 unrefined oC 171.06 406.09 208.80 59.1 90.0 104.1 C222,C2221
27 398 unrefined tI 269.92 238.92 200.20 75.3 73.2 88.9 I4,I41,I422,I4122
26 384 unrefined oC 238.76 285.79 208.80 111.4 115.9 80.9 C222,C2221
25 375 unrefined hR 238.76 238.92 413.27 103.5 76.5 128.2 H3,H32 (hexagonal settings of R3 and R32)
200.20 171.06 200.37 79.6 57.7 79.6 R3,R32 (primitive rhombohedral cell)
24 372 unrefined tP 200.20 208.80 171.06 90.0 100.4 121.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
23 361 unrefined oI 171.06 208.80 348.51 89.9 73.5 90.0 I222,I212121
22 360 unrefined mC 406.09 171.06 208.80 90.0 120.9 75.9 C2
21 334 unrefined oP 171.06 200.20 208.80 121.4 90.0 100.4 P222,P2221,P21212,P212121
20 333 unrefined oI 238.92 269.92 200.20 73.2 75.3 88.9 I222,I212121
19 310 unrefined mC 285.79 238.76 200.37 104.7 115.3 80.9 C2
18 295 unrefined mC 285.79 238.76 269.93 88.8 137.9 80.9 C2
17 269 unrefined mP 171.06 208.80 200.20 121.4 100.4 90.0 P2,P21
16 268 unrefined mP 171.06 208.80 200.20 121.4 100.4 90.0 P2,P21
15 245 unrefined mC 285.79 238.76 200.37 75.3 115.3 99.1 C2
14 218 unrefined mC 406.09 171.06 208.80 90.0 120.9 75.9 C2
13 218 unrefined oI 171.06 208.80 348.51 90.1 106.5 90.0 I222,I212121
12 218 unrefined mI 269.92 348.51 171.06 106.5 129.3 79.7 C2 (transformed from I2)
11 217 unrefined mC 406.09 171.06 208.80 90.0 120.9 75.9 C2
10 141 0.501 0.99 hP 208.80 200.37 171.06 100.4 90.0 121.5 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
9 140 0.355 0.99 oC 200.20 356.94 171.06 84.2 100.4 87.2 C222,C2221
8 140 0.326 0.99 mC 200.20 356.94 171.06 84.2 100.4 87.2 C2
7 104 0.233 0.97 oC 208.80 341.85 171.06 77.8 90.0 89.9 C222,C2221
6 102 0.326 0.99 mC 200.20 356.94 171.06 84.2 100.4 87.2 C2
5 102 0.412 0.97 mP 200.20 171.06 208.80 90.0 121.4 100.4 P2,P21
4 38 0.057 0.89 mC 341.85 208.80 171.06 90.0 102.2 90.1 C2
3 37 0.059 0.89 aP 171.06 200.20 208.80 121.4 90.0 100.4 P1
2 1 0.057 0.89 mC 341.85 208.80 171.06 90.0 102.2 90.1 C2
1 0 0.059 0.89 aP 171.06 200.20 200.37 62.8 79.6 79.6 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
Suggested Solution: 2 C2
penalty: 1
cell: 341.850 208.795 171.063 90.00 102.17 90.06
regularized cell: 341.850 208.795 171.063 90.00 102.17 90.00
Symmetry: mC (C Centred Monoclinic)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /opt/pxsoft/ccp4-6.0/lib/data/syminfo.lib
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /opt/pxsoft/ccp4-6.0/lib/data/syminfo.lib
Mosflm has chosen solution 2 from the list automatically. You may want to
re-run the autoindexing and choose a solution yourself.
The solution and direct beam position will now be refined; reflections which
deviate by more than the sigma cutoff from their calculated position will
be excluded from the refinement.
Refining solution # 2 with C2 (number 5) symmetry imposed
Initial cell (before refinement) is 341.8503 208.7951 171.0627 90.000 102.175 90.000
Using 90 indexed reflections (out of 101 spots used in indexing, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.06mm and in phi 0.17 degrees
Refined cell parameters 342.01 208.71 171.08 90.00 102.14 90.00
Beam coordinates of 156.94 158.85 have been refined to 156.88 158.75
This is a shift of 0.12mm or 0.142 times the minimum spot separation of ca 0.84mm.
Final cell (after refinement) is 342.0149 208.7128 171.0817 90.000 102.140 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_002.img
**** Information ****
**** Information ****
**** Information ****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 1.0050) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-srpol-HA00AG3240_1
Warning: No PROTEIN NAME given by KeyWord PNAME
It has been set to "Unspecified"
Warning: No CRYSTAL NAME given by KeyWord XNAME
It has been set to "ref-srpol-HA00AG3240_1"
Warning: No DATASET NAME given by KeyWord DNAME
It has been set to "Unspecified"
PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000
MAX. No. of Active Reflections= 100
Beam divergence refinement
Too many reflections generated; temporarily reducing resolution to 1.816
(it will revert to 1.513 after mosaicity estimation)
PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000
MAX. No. of Active Reflections= 100
Beam divergence refinement
Too many reflections generated; temporarily reducing resolution to 2.179
(it will revert to 1.513 after mosaicity estimation)
PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000
MAX. No. of Active Reflections= 100
Beam divergence refinement
Beam divergence refinement
Refining DIV with stepsize 0.01 Degrees
Divergence 0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800
Divergence 1.900 2.000
No gained 1001 1593 1598 1506 1492 1526 1390 1422 1445 1414 1308 523 509 442 407 368 375 353 310
No gained 307 267
Total intensity 59810 69692 75495 79887 83076 87206 90343 93009 95885 97819 99963 99231 97715 96931 95780 94107 93271 91964 90500
Total intensity 88879 87154
SD of intensity 993 1098 1202 1307 1359 1464 1516 1568 1673 1725 1778 1725 1725 1725 1673 1673 1673 1621 1621
SD of intensity 1621 1568
The mosaicity has been estimated as ---> 0.77 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: C2 number 5
Storing space group from DPS autoindexing: C2 number 5
===> BEST OFF
===> xgui on
New gui stuff switched on
===> image 1
===> go
Start and end phi values for image 1 from image header are 0.00 and 0.50 degrees.
Oscillation axis set as PHI from image header
***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
Input beam coordinates 156.88mm 158.75mm DO NOT agree with
those calculated from the image header ( 156.94mm 158.85mm)
Warning - resetting the iseg value to zero because gui_switch = .true.
image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_001.img
NeoCtrl => ===> predict_spots
Predicted
0 fulls
28698 partials
2195 wides
12168 overlaps
NeoCtrl => ===> create_image binary true filename ref-srpol-HA00AG3240_1_001.jpg
Output filename set to ref-srpol-HA00AG3240_1_001.jpg
Beam centre = 156.878571 158.746552
Calling write_jpeg with arg list:
trc = 0 0
blc = 3072 3072
factor = 1
write_jpeg -1 3072 3072 0 0
1 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took: 1.121
Returning from CREATE_IMAGE after 2.427 seconds
NeoCtrl => ===> create_image prediction on binary true filename ref-srpol-HA00AG3240_1_001_pred.jpg
Output filename set to ref-srpol-HA00AG3240_1_001_pred.jpg
Beam centre = 156.878571 158.746552
writing binary jpeg
writing predictions
writing a nice binary JPEG with predictions
box sizes are 6 6
zoom is 1
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after 2.907 seconds
NeoCtrl => ===> create_image zoom -4 binary true filename ref-srpol-HA00AG3240_1_001_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_001_small.jpg
Beam centre = 156.878571 158.746552
Calling write_jpeg with arg list:
trc = 0 0
blc = 3072 3072
factor = -4
write_jpeg -1 3072 3072 0 0
-4 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took: 0.059
Returning from CREATE_IMAGE after 0.292 seconds
NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-srpol-HA00AG3240_1_001_pred_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_001_pred_small.jpg
Beam centre = 156.878571 158.746552
writing binary jpeg
writing predictions
writing a nice binary JPEG with predictions
box sizes are 1 1
zoom is -4
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after 0.442 seconds
NeoCtrl => ===> return
New gui stuff switched off
===> xgui off
New gui stuff switched off
===> xgui on
New gui stuff switched on
===> image 2
===> go
Start and end phi values for image 2 from image header are 89.50 and 90.00 degrees.
Oscillation axis set as PHI from image header
***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
Input beam coordinates 156.88mm 158.75mm DO NOT agree with
those calculated from the image header ( 156.94mm 158.85mm)
Warning - resetting the iseg value to zero because gui_switch = .true.
image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_002.img
NeoCtrl => ===> predict_spots
Predicted
0 fulls
32981 partials
2091 wides
8181 overlaps
NeoCtrl => ===> create_image binary true filename ref-srpol-HA00AG3240_1_002.jpg
Output filename set to ref-srpol-HA00AG3240_1_002.jpg binary true filename ref-srpol-HA00AG3240_1_001_pred_small.jpg
Beam centre = 156.878571 158.746552
Calling write_jpeg with arg list:
trc = 0 0
blc = 3072 3072
factor = 1
write_jpeg -1 3072 3072 0 0
1 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took: 1.119
Returning from CREATE_IMAGE after 2.393 seconds
NeoCtrl => ===> create_image prediction on binary true filename ref-srpol-HA00AG3240_1_002_pred.jpg
Output filename set to ref-srpol-HA00AG3240_1_002_pred.jpg filename ref-srpol-HA00AG3240_1_001_pred_small.jpg
Beam centre = 156.878571 158.746552
writing binary jpeg
writing predictions
writing a nice binary JPEG with predictions
box sizes are 6 6
zoom is 1
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after 2.923 seconds
NeoCtrl => ===> create_image zoom -4 binary true filename ref-srpol-HA00AG3240_1_002_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_002_small.jpg filename ref-srpol-HA00AG3240_1_001_pred_small.jpg
Beam centre = 156.878571 158.746552
Calling write_jpeg with arg list:
trc = 0 0
blc = 3072 3072
factor = -4
write_jpeg -1 3072 3072 0 0
-4 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took: 0.060
Returning from CREATE_IMAGE after 0.294 seconds
NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-srpol-HA00AG3240_1_002_pred_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_002_pred_small.jpg
Beam centre = 156.878571 158.746552
writing binary jpeg
writing predictions
writing a nice binary JPEG with predictions
box sizes are 1 1
zoom is -4
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after 0.396 seconds
NeoCtrl => ===> return
New gui stuff switched off
===> xgui off
New gui stuff switched off
*********** END OF PROCESSING *****************