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This reports processing of triclinic hen egg-white lysozyme data @ 0.65Å resolution (PDB id [[2VB1]]). Data (sweeps a to h, each comprising 60 to 360 frames of 72MB) were collected by Zbigniew Dauter at APS 19-ID and are available from [http://bl831.als.lbl.gov/example_data_sets/APS/19-ID/2vb1/ here]. Details of data collection, processing and refinement are [http://journals.iucr.org/d/issues/2007/12/00/be5097/index.html published].  
This reports processing of triclinic hen egg-white lysozyme data @ 0.65Å resolution (PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1 2VB1]). Data (sweeps a to h, each comprising 60 to 360 frames of 72MB) were collected by Zbigniew Dauter at APS 19-ID and are available from [http://bl831.als.lbl.gov/example_data_sets/APS/19-ID/2vb1/ here]. Details of data collection, processing and refinement are [http://journals.iucr.org/d/issues/2007/12/00/be5097/index.html published].  


== XDS processing ==
== XDS processing ==


 
# use [[generate_XDS.INP]] to obtain a good starting point
* use [[generate_XDS.INP]] to obtain a good starting point
# edit [[XDS.INP]] and change/add the following:
* edit [[XDS.INP]] and change the following:
  ORGX=3130 ORGY=3040  ! for ADSC, header values are subject to interpretation; these values from visual inspection
  ORGX=3130 ORGY=3040  ! for ADSC, header values are subject to interpretation; better inspect the table in IDXREF.LP!
! the following is for masking the beamstop shadow in sweeps c-d
UNTRUSTED_RECTANGLE=0 3189 2960 3087 ! use XDS-viewer of ADXV to find the values
! the following is for sweeps e-h
UNTRUSTED_RECTANGLE=1 3160 3000 3070
  TRUSTED_REGION=0 1.5 ! we want the whole detector area
  TRUSTED_REGION=0 1.5 ! we want the whole detector area
  ROTATION_AXIS=-1 0 0 ! at this beamline the spindle goes backwards!
  ROTATION_AXIS=-1 0 0 ! at this beamline the spindle goes backwards!
* for faster processing on a machine with many cores, use (e.g. for 16 cores):
SILICON=34.812736 ! account for theta-dependant absorption in the CCD's phosphor. The correction is only
  MAXIMUM_NUMBER_OF_PROCESSORS=2
! significant for hi-res data; 34.812736=32*(value for silicon as printed to CORRECT.LP if SILICON= not given)
  MAXIMUM_NUMBER_OF_JOBS=8
MAXIMUM_NUMBER_OF_PROCESSORS=4 ! for fast processing on a machine with many cores (e.g. for 16 cores)
  MAXIMUM_NUMBER_OF_JOBS=6 ! "overcommit" the available cores but on the whole this produces results faster
SPACE_GROUP_NUMBER=1                  ! this is known
  UNIT_CELL_CONSTANTS=  27.07 31.25 33.76 87.98 108.00 112.11  ! from 2vb1
FRIEDEL'S_LAW=TRUE  ! we're not concerned with the anomalous signal


For all the sweeps, processing stopped with an [[Problems#IDXREF_ends_with_message|error message]] after the IDXREF step. By inspecting IDXREF.LP, one should make sure that everything works as it should, i.e. that a large percentage of reflections was actually indexed nicely:
Then, run "xds_par". It completes after about 5 minutes on a fast machine, and we may inspect (at least) IDXREF.LP and CORRECT.LP (see below), and use "XDS-viewer FRAME.cbf" to get a visual impression of the integration as it applies to the last frame.
By inspecting IDXREF.LP, one should make sure that everything works as it should, i.e. that a large percentage of reflections was actually indexed nicely, e.g.:


  ...
  ...
Line 26: Line 34:
  STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.12
  STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.12
   
   
It may be possible to adjust some parameters (for COLSPOT) so that the error message does not occur, but it is not worth the effort. So we just change
=== Optimization ===
  JOBS=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 
to
The main target of optimization is the asymptotic (i.e. best) I/sigma (ISa) (Diederichs (2010) [http://dx.doi.org/10.1107/S0907444910014836 Acta Cryst. D 66, 733-40]) as printed out by CORRECT (and XSCALE). A higher ISa should mean better data.
  JOBS=DEFPIX INTEGRATE CORRECT
 
and run "xds_par" again. It completes after about 5 minutes on a fast machine, and we may inspect CORRECT.LP .
However: ISa also rises if more reflections are thrown out as outliers ("misfits") so it is not considered to be optimization if just WFAC1 is reduced. Please note that the default WFAC1 is 1; this should result in the rejection of about 1% of observations. If you feel that 1% is too much then just increase WFAC1, to, say, 1.5 - that should result in rejection of less than (say) 0.1%. This will slightly increase completeness, but will reduce I/sigma and ISa, and increase R-factors.
 
The following quantities may be tested for their influence on ISa:
* copying GXPARM.XDS to XPARM.XDS
* including the information from the first integration pass into XDS.INP - just do "grep _E INTEGRATE.LP|tail -2" and get e.g.
  BEAM_DIVERGENCE=  0.386  BEAM_DIVERGENCE_E.S.D.=  0.039
REFLECTING_RANGE=  0.669  REFLECTING_RANGE_E.S.D.=  0.096
copy these two lines into XDS.INP
* prevent refinement in INTEGRATE: REFINE(INTEGRATE)= !
 
== Example: sweep e ==
=== [[XDS.INP]]; as generated by [[generate_XDS.INP]] ===
 
generate_XDS.INP "../../APS/19-ID/2vb1/p1lyso_e.0???.img"
 
Then include the changes detailed above, resulting in:
 
<pre>
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
MAXIMUM_NUMBER_OF_PROCESSORS=4
MAXIMUM_NUMBER_OF_JOBS=6
ORGX= 3130 ORGY= 3040  ! check these values with adxv !
UNTRUSTED_RECTANGLE=1 3160 3000 3070  ! <xmin xmax ymin ymax> to mask shadow of beamstop; XDS-viewer to find out
DETECTOR_DISTANCE= 99.9954
OSCILLATION_RANGE= 0.500
X-RAY_WAVELENGTH=  0.6525486
NAME_TEMPLATE_OF_DATA_FRAMES=../../APS/19-ID/2vb1/p1lyso_e.0???.img
! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing 
DATA_RANGE=1 360
SPOT_RANGE=1 180
! BACKGROUND_RANGE=1 10 ! rather use defaults (first 5 degree of rotation)
 
SPACE_GROUP_NUMBER=1                  ! 0 if unknown
UNIT_CELL_CONSTANTS= 27.07    31.25    33.76  87.98 108.00 112.11  ! PDB 2vb1
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT
 
 
!FRIEDEL'S_LAW=FALSE    ! This acts only on the CORRECT step
! If the anom signal turns out to be, or is known to be, very low or absent,
! use FRIEDEL'S_LAW=TRUE instead (or comment out the line); re-run CORRECT
 
! remove the "!" in the following line:
! STRICT_ABSORPTION_CORRECTION=TRUE
! if the anomalous signal is strong: in that case, in CORRECT.LP the three
! "CHI^2-VALUE OF FIT OF CORRECTION FACTORS" values are significantly> 1, e.g. 1.5
!
! exclude (mask) untrusted areas of detector, e.g. beamstop shadow :
! UNTRUSTED_RECTANGLE= 1800 1950 2100 2150 ! x-min x-max y-min y-max ! repeat
! UNTRUSTED_ELLIPSE= 2034 2070 1850 2240 ! x-min x-max y-min y-max ! if needed
!
! parameters with changes wrt default values:
TRUSTED_REGION=0.00 1.5  ! partially use corners of detectors; 1.41421=full use
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok
MINIMUM_ZETA=0.05        ! integrate close to the Lorentz zone; 0.15 is default
STRONG_PIXEL=6          ! COLSPOT: only use strong reflections (default is 3)
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE
 
! parameters specifically for this detector and beamline:
DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000
SENSOR_THICKNESS=0.01 SILICON=34.812736
NX= 6144 NY= 6144  QX= 0.051294  QY= 0.051294 ! to make CORRECT happy if frames are unavailable
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
INCIDENT_BEAM_DIRECTION=0 0 1
ROTATION_AXIS=-1 0 0    ! at e.g. SERCAT ID-22 this needs to be -1 0 0
FRACTION_OF_POLARIZATION=0.98  ! better value is provided by beamline staff!
POLARIZATION_PLANE_NORMAL=0 1 0
 
</pre>
 
=== [[CORRECT.LP]] 1st pass ===
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)    0.87
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.10
CRYSTAL MOSAICITY (DEGREES)    0.126
...
    a        b          ISa
6.630E+00  1.091E-04  37.18
...
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION    NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR COMPARED I/SIGMA  R-meas  Rmrgd-F  Anomal  SigAno  Nano
  LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
    1.77        9195    4841      9501      51.0%      1.5%      1.5%    8708  48.74    2.1%    1.6%    0%  0.000      0
    1.26      29991  15327    16721      91.7%      1.5%      1.6%    29328  45.26    2.1%    1.7%    0%  0.000      0
    1.03      38643  19731    21636      91.2%      1.7%      1.7%    37824  38.67    2.5%    2.1%    0%  0.000      0
    0.89      46156  23404    25561      91.6%      2.3%      2.4%    45504  27.56    3.3%    3.4%    0%  0.000      0
    0.80      51509  26034    28868      90.2%      4.0%      4.0%    50950  17.55    5.6%    7.0%    0%  0.000      0
    0.73      55989  28253    32034      88.2%      7.0%      6.8%    55472  10.98    9.8%    13.2%    0%  0.000      0
    0.68      59733  30115    34776      86.6%      13.1%    13.0%    59236    6.08    18.6%    26.0%    0%  0.000      0
    0.63      35385  18436    37367      49.3%      25.6%    26.9%    33898    2.99    36.3%    52.1%    0%  0.000      0
    0.60        8991    4972    39725      12.5%      51.2%    56.9%    8038    1.34    72.4%  105.0%    0%  0.000      0
    total      335592  171113    246189      69.5%      2.3%      2.4%  328958  19.58    3.3%    7.4%    0%  0.000      0
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  343716
NUMBER OF REJECTED MISFITS                            8112
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
NUMBER OF ACCEPTED OBSERVATIONS                    335604
NUMBER OF UNIQUE ACCEPTED REFLECTIONS              171119
 
The number of "misfits" (rejections) is higher than expected (1 %). Either one considers the anomalous signal (of the 6 sulfurs) to be significant, or one simply increases WFAC1 from its default of 1, to (say) 1.2 .
 
=== [[XDS.INP]]; optimized ===
Using the output of "grep _E INTEGRATE.LP|tail -2" edit XDS.INP to have
  JOB= INTEGRATE CORRECT
BEAM_DIVERGENCE=  0.428  BEAM_DIVERGENCE_E.S.D.=  0.043
REFLECTING_RANGE=  0.880  REFLECTING_RANGE_E.S.D.=  0.126
...
REFINE(INTEGRATE)= !
 
Then "cp GXPARM.XDS XPARM.XDS", and then another round of "xds_par". Five minutes later, we get:
 
=== [[CORRECT.LP]] optimization pass ===
 
This looks a little bit better - less standard deviation, higher ISa, better R-factors, less misfits:
 
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)    0.83
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.08
CRYSTAL MOSAICITY (DEGREES)    0.096
    a        b          ISa
6.439E+00  1.076E-04  37.98
...
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION    NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR COMPARED I/SIGMA  R-meas  Rmrgd-F  Anomal  SigAno  Nano
  LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
    1.77        9149    4817      9501      50.7%      1.5%      1.5%    8664  49.75    2.1%    1.5%    0%  0.000      0
    1.26      30049  15348    16723      91.8%      1.5%      1.6%    29402  46.26    2.1%    1.6%    0%  0.000      0
    1.03      38920  19863    21637      91.8%      1.7%      1.7%    38114  39.61    2.4%    2.0%    0%  0.000      0
    0.89      46381  23508    25562      92.0%      2.2%      2.3%    45746  28.39    3.1%    3.2%    0%  0.000      0
    0.80      51605  26071    28868      90.3%      3.8%      3.8%    51068  18.21    5.3%    6.5%    0%  0.000      0
    0.73      56126  28314    32041      88.4%      6.6%      6.4%    55624  11.45    9.3%    12.3%    0%  0.000      0
    0.68      59735  30093    34771      86.5%      12.6%    12.3%    59284    6.34    17.8%    24.8%    0%  0.000      0
    0.63      35754  18620    37370      49.8%      24.1%    25.5%    34268    3.11    34.1%    48.9%    0%  0.000      0
    0.60        9180    5075    39730      12.8%      48.6%    54.3%    8210    1.40    68.7%  100.5%    0%  0.000      0
    total      336899  171709    246203      69.7%      2.2%      2.3%  330380  20.14    3.2%    6.9%    0%  0.000      0
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  344751
NUMBER OF REJECTED MISFITS                            7842
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
NUMBER OF ACCEPTED OBSERVATIONS                    336909
NUMBER OF UNIQUE ACCEPTED REFLECTIONS              171714


== timings for processing sweep "e" as a function of MAXIMUM_NUMBER_OF_PROCESSORS and MAXIMUM_NUMBER_OF_JOBS ==
=== further optimization ===


The following is going to be rather technical! If you are only interested in crystallography, skip this.
Another round of optimization again improves the R-factors and I/sigma at high resolution a bit, but it also increased the misfits back to 8200. At this point I decided to switch to FRIEDEL'S_LAW=FALSE, and the resulting table is:
      NOTE:      Friedel pairs are treated as different reflections.
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION    NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR COMPARED I/SIGMA  R-meas  Rmrgd-F  Anomal  SigAno  Nano
  LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
    1.77        9599    9023    19002      47.5%      1.5%      1.5%    1152  36.81    2.1%    1.6%    0%  0.000      0
    1.26      31196  28239    33446      84.4%      1.4%      1.6%    5914  34.40    2.0%    1.6%    0%  0.000      0
    1.03      40125  35205    43274      81.4%      1.7%      1.7%    9840  30.09    2.4%    2.0%    0%  0.000      0
    0.89      46987  40188    51124      78.6%      2.3%      2.3%    13598  22.03    3.2%    3.4%    0%  0.000      0
    0.80      52229  43723    57738      75.7%      3.9%      3.9%    17012  14.44    5.5%    6.6%    0%  0.000      0
    0.73      56830  46674    64088      72.8%      7.1%      6.8%    20312    9.30    10.1%    13.2%    0%  0.000      0
    0.68      60488  48814    69544      70.2%      13.9%    13.5%    23348    5.26    19.6%    27.1%    0%  0.000      0
    0.63      36190  28598    74736      38.3%      28.2%    29.7%    15184    2.70    39.8%    57.3%    0%  0.000      0
    0.60        9246    7246    79466        9.1%      57.8%    62.4%    4000    1.26    81.8%  122.0%    0%  0.000      0
    total      342890  287710    492418      58.4%      2.8%      2.8%  110360  16.19    3.9%    9.9%    0%  0.000      0
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  345355
NUMBER OF REJECTED MISFITS                            2448
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS                  0
NUMBER OF ACCEPTED OBSERVATIONS                    342907
NUMBER OF UNIQUE ACCEPTED REFLECTIONS              287724


Using
Indeed this brings the number of misfits to well below 1%, and it does make some sense.
MAXIMUM_NUMBER_OF_PROCESSORS=2
MAXIMUM_NUMBER_OF_JOBS=8
we observe for the INTEGRATE step:
total cpu time used              2063.6 sec
total elapsed wall-clock time      296.1 sec


Using
== XSCALE results ==
MAXIMUM_NUMBER_OF_PROCESSORS=1
MAXIMUM_NUMBER_OF_JOBS=16
the times are
total cpu time used              2077.1 sec
total elapsed wall-clock time      408.2 sec


Using
The same strategy as shown for sweep e was used for sweeps a-d and f-h. XSCALE.INP is:
MAXIMUM_NUMBER_OF_PROCESSORS=4
MAXIMUM_NUMBER_OF_JOBS=4
the times are
total cpu time used               2102.8 sec
total elapsed wall-clock time      315.6 sec


Using
  SPACE_GROUP_NUMBER=   1
  MAXIMUM_NUMBER_OF_PROCESSORS=16 ! the default for xds_par on a 16-core machine
  UNIT_CELL_CONSTANTS= 27.07 31.25 33.76 87.98 108.00 112.11 !  from 2vb1 PDB entry
  MAXIMUM_NUMBER_OF_JOBS=1 ! the default
  ! cellparm for a-h gives  27.083    31.269    33.773    87.978  107.998  112.133
the times are
  total cpu time used              2833.4 sec
  total elapsed wall-clock time      566.5 sec


Using
OUTPUT_FILE=lys-xds.ahkl
  MAXIMUM_NUMBER_OF_PROCESSORS=4
  FRIEDEL'S_LAW=TRUE
  MAXIMUM_NUMBER_OF_JOBS=8
  RESOLUTION_SHELLS=2.91 2.06 1.68 1.45 1.30 1.19 1.10 1.03 0.97 0.92 0.88 0.84 0.81 0.78 0.75 0.73 0.71 0.69 0.67 0.65
(thus overcommitting the available cores by a factor of 2) the times are
  total cpu time used              2263.5 sec
INPUT_FILE=../a/XDS_ASCII.HKL
  total elapsed wall-clock time      320.8 sec
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../b/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../c/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../d/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../e/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../f/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../g/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
INPUT_FILE=../h/XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=30 0.65
 
=== XSCALE.LP tables ===
 
The error model is adjusted by XSCALE:
    a        b          ISa    ISa0  INPUT DATA SET
7.094E+00  1.294E-04  33.00  38.03 ../a/XDS_ASCII.HKL                               
7.476E+00  1.170E-04  33.81  38.95 ../b/XDS_ASCII.HKL                               
7.453E+00  1.598E-04  28.98  38.00 ../c/XDS_ASCII.HKL                               
6.539E+00  1.640E-04  30.54  39.08 ../d/XDS_ASCII.HKL                               
  7.304E+00  1.342E-04  31.94  37.69 ../e/XDS_ASCII.HKL                               
  8.201E+00  1.574E-04  27.83  35.58 ../f/XDS_ASCII.HKL                               
8.182E+00  1.759E-04  26.36  27.60 ../g/XDS_ASCII.HKL                               
7.717E+00  3.694E-04  18.73  21.93 ../h/XDS_ASCII.HKL                               
and there are about 1500 rejected reflections. It is reassuring to note that the error model works well; the ISa goes down toward sweep h probably because the crystal degrades. But see also the "a posterior remarks" below - sweep h is the one that is most affected by a shadow on the detector.


Using
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
  MAXIMUM_NUMBER_OF_PROCESSORS=4
  RESOLUTION    NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR COMPARED I/SIGMA  R-meas  Rmrgd-F  Anomal  SigAno  Nano
MAXIMUM_NUMBER_OF_JOBS=6
  LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
(thus overcommitting the available cores, but less severely) the times are
total cpu time used              2367.6 sec
    2.91      16170    2112      2147      98.4%      2.2%      2.4%    16157  78.96    2.5%    1.1%  -12%  0.741    2023
  total elapsed wall-clock time     267.2 sec
    2.06      40349    3831      3856      99.4%      2.4%      2.7%    40345  84.89    2.6%    0.9%    -9%  0.764    3803
    1.68      65329    5068      5087      99.6%      3.1%      3.2%    65321  83.77    3.3%    1.0%    0%  0.847    5020
    1.45      73373    6147      6163      99.7%      3.2%      3.5%    73371  78.02    3.4%    1.0%    2%  0.842    6053
    1.30      71196    6651      6657      99.9%      3.2%      3.5%    71196  71.07    3.4%    1.1%    4%  0.857    6503
    1.19      74542    7287      7298      99.8%      3.2%      3.4%    74534  67.06    3.3%    1.2%    5%  0.854    7060
    1.10      84918    8269      8278      99.9%      3.4%      3.7%    84891  63.24    3.6%    1.3%    7%  0.853    7988
    1.03      87890    8584      8603      99.8%      4.1%      4.4%    87855  56.26    4.4%    1.5%    5%  0.818    8231
    0.97      92917    9460      9465      99.9%      5.2%      5.6%    92894  48.90    5.5%    1.7%    4%  0.795    9010
    0.92      83994    9911      9927      99.8%      5.7%      6.3%    83969  41.67    6.0%    2.0%    6%  0.787    9358
    0.88      74100    9620      9621      100.0%      6.3%      7.1%    74082  35.74    6.7%    2.5%    4%  0.772    9040
    0.84      81322  11511    11518      99.9%      6.9%      7.7%    81300  30.43    7.3%    3.3%    1%  0.760  10609
    0.81      67539  10239    10247      99.9%      7.1%      7.7%    67518  25.96    7.7%    4.2%    2%  0.779    9364
    0.78      73980  11807    11817      99.9%      7.1%      7.3%    73951  22.34    7.7%    5.3%    2%  0.799  10699
    0.75      86111  13831    13839      99.9%      8.4%      8.6%    86076  18.77    9.2%    6.8%    2%  0.809  12496
    0.73      64554  10481    10488      99.9%      10.3%    10.4%    64525  15.73    11.3%    8.2%    3%  0.815    9384
    0.71      71891  11727    11741      99.9%      12.8%    13.0%    71844  12.95    14.0%    10.6%    3%  0.810  10436
    0.69      80168  13157    13163      100.0%      16.6%    16.9%    80065  10.16    18.2%    14.1%    2%  0.799  11662
    0.67      84431  14747    14766      99.9%      22.2%    22.7%    84231    7.44    24.4%    19.7%    3%  0.798  12520
    0.65      61031  15592    16551      94.2%      27.6%    30.6%    60165    4.36    31.8%    33.1%    1%  0.723    9005
    total    1435805 190032    191232      99.4%      3.1%     3.3%  1434290  33.42    3.3%    3.1%    3%  0.801  170264


Thus,  
If two more resolution shells are added, they look like -
MAXIMUM_NUMBER_OF_PROCESSORS=4
    0.64      23276    7411      9155      81.0%      35.0%    40.6%    22324    2.90    41.7%    47.9%    3%  0.683    3204
MAXIMUM_NUMBER_OF_JOBS=6
    0.63      18044    6488      9647      67.3%      42.2%    49.7%    16630    2.22    50.7%    60.9%    -5%  0.643    2437
performs best for a 2-Xeon X5570 machine with 24GB of memory and a RAID1 consisting of 2 1TB SATA disks. It should be noted that the dataset has 27GB, and in 296 seconds this means 92 MB/s continuous reading. The processing time is thus limited by the disk access, not by the CPU. And no, the data are not simply read from RAM (tested by "echo 3 > /proc/sys/vm/drop_caches before the XDS run).
So there is still useful signal beyond 0.65 A.


== Some ''a posteriori'' remarks ==


== Comparison of XDS and published results of data processing ==
* For sweeps e-h one should use TRUSTED_REGION= 0 1.2 since that already gives 0.626 A in the corners.


* The first and last frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so at least if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). <br> One could experiment with MINIMUM_VALID_PIXEL_VALUE= 40 (or so) instead of 1 - I'd probably try that, but of course one does not want to exclude valid pixels so the result has to be carefully checked. <br> Anyway, there is no general facility in XDS to exclude bad areas of ''specific'' frames in a dataset; one needs to chop the dataset into parts and deal with each shadow separately.
== Comparison of data processing: published (2006) ''vs'' XDS results ==


<table border = "1">
<table border = "1">


<tr>
<tr><b>
<b>
<td> </td>
<td>completeness overall (30-0.65Å (%)</td>
<td> resolution (highest resolution range)
<td>data redundancy</td>
<td> observations </td>
<td>R merge</td>
<td> unique reflections </td>
<td><I/sigma></td>
<td> Multiplicity </td>
<td>completeness in highest resolution range (0.67-0.65Å)</td>
<td> Completeness (%) </td>
<td>data redundancy in highest resolution range (0.67-0.65Å)</td>
<td> R merge (%) </td>
<td>R merge in highest resolution range</td>
<td> mean I/sigma </td>
<td><I/sigma> in highest resolution range</td>
</b></tr>
</b></tr>


<tr>
<tr><b>
<td>Hampton PEG/ion #1</td>
<td> published (2006) </td>
<td>0.2M NaF, 20% PEG3350, pH7.1</td>
<td> 30-0.65Å (0.67-0.65Å) </td>
<td>10mM Tris pH7.5, 150mM NaCl</td>
<td> 1331953 (12764) </td>
<td>yes</td>
<td> 187165 (6353) </td>
<td>I've seen this condition produce salt crystals at least twice.--[[User:Pozharski|Ed]] 16:18, 23 May 2008 (CEST) <br> Ditto - NaF has caused me trouble many times - buyer beware! [[User:DaveB|DaveB]] 11:01, 24 May 2008 (CEST) </td>
<td> 7.1 (2.7) </td>
<td>Hampton PEG/ion #1</td>
<td> 97.6 (67.3) </td>
<td>0.2M NaF, 20% PEG3350, pH7.1</td>
<td> 4.5 (18.4) </td>
<td>10mM Tris pH7.5, 150mM NaCl</td>
<td> 36.2 (4.2) </td>
<td>yes</td>
</b></tr>
<td>I've seen this condition produce salt crystals at least twice.--[[User:Pozharski|Ed]] 16:18, 23 May 2008 (CEST) <br> Ditto - NaF has caused me trouble many times - buyer beware! [[User:DaveB|DaveB]] 11:01, 24 May 2008 (CEST) </td>
 
<tr><b>
<td> XDS Version Dec 06, 2010 </td>
<td> 30-0.65Å (0.67-0.65Å) </td>
<td> 1435805 (61031) </td>
<td> 190032 (15592) </td>
<td> 7.5 (3.9) </td>
<td> 99.4 (94.2) </td>
<td> 3.1 (27.6) </td>
<td> 33.4 (4.4) </td>
</b></tr>


</table>
</table>


REMARK 200 COMPLETENESS FOR RANGE    (%) : 97.6                             
== Availability of data from XDS processing ==
REMARK 200 DATA REDUNDANCY                : 7.1                              
I changed XSCALE.INP to have
REMARK 200  R MERGE                    (I) : 0.04                             
  !FRIEDEL'S_LAW=TRUE  ! by commenting it out XSCALE will use FRIEDEL'S_LAW=FALSE
REMARK 200  R SYM                      (I) : NULL                             
!                      since this is how the data were processed
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.20                             
  RESOLUTION_SHELLS=2.91 2.06 1.68 1.45 1.30 1.19 1.10 1.03 0.97 0.92 0.88 0.84 0.80 0.76 0.73 0.70 0.67 0.65 0.64 0.63
REMARK 200                                                                     
 
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                   
and ran XSCALE again, to get a file with reflections to 0.63 A.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.65                   
 
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.67                   
Conversion to other program systems is performed with XDSCONV. XDSCONV.INP for producing a MTZ file with intensities and anomalous signal is:
REMARK 200 COMPLETENESS FOR SHELL    (%) : 67.3                             
  INPUT_FILE= lys-xds.ahkl
REMARK 200 DATA REDUNDANCY IN SHELL      : 2.7                               
  OUTPUT_FILE=temp.hkl CCP4_I
REMARK 200 R MERGE FOR SHELL          (I) : 0.18                             
 
REMARK 200  R SYM FOR SHELL            (I) : NULL                             
After running xdsconv, I cut-and-paste the screen output:
REMARK 200  <I/SIGMA(I)> FOR SHELL        : 4.20
  f2mtz HKLOUT temp.mtz<F2MTZ.INP
  cad HKLIN1 temp.mtz HKLOUT output_file_name.mtz<<EOF
  LABIN FILE 1 ALL
  END
  EOF
 
and obtain output_file_name.mtz which I mv to [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-I.mtz xds-hewl-I.mtz]. SFCHECK statistics for this file are [https://{{SERVERNAME}}/pub/xds-datared/2vb1/sfcheck_XXXX.pdf here].
 
Similarly, using OUTPUT_FILE=temp.hkl CCP4 I obtained a file with amplitudes, [https://{{SERVERNAME}}/pub/xds-datared/2vb1/xds-hewl-F.mtz xds-hewl-F.mtz]
Retrieved from "https://wiki.uni-konstanz.de/xds/index.php/Special:MobileDiff/2328...4081"
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