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Revision as of 23:51, 25 December 2016

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== Round 1: processing the data, and determining the space group ==
Using
<pre>
#!/bin/bash -f
for f in `seq 1 100`;
do
export OUT=wedge0`printf "%03d" $f`
export NAMES="$PWD/Illuin/microfocus/xtal"`printf "%03d" $f`"_1_00\?.img"
rm -rf $OUT
mkdir $OUT
cd $OUT
generate_XDS.INP $NAMES
sed -i s"/SPOT_RANGE=1 1/SPOT_RANGE=1 3/" XDS.INP
sed -i s"/SPACE_GROUP_NUMBER=0/SPACE_GROUP_NUMBER=1/" XDS.INP
sed -i s"/UNIT_CELL_CONSTANTS= 70 80 90/UNIT_CELL_CONSTANTS=38.3 79.1 79.1/" XDS.INP
sed -i s"/TRUSTED_REGION=0.0 1.2/TRUSTED_REGION=0 1/" XDS.INP
sed -i s"/INCLUDE_RESOLUTION_RANGE=50 0/INCLUDE_RESOLUTION_RANGE=99 1.8/" XDS.INP
/usr/local/bin/xds_par
cd ..
done
mkdir xscale
cd xscale
cat >XSCALE.INP <<eof
SPACE_GROUP_NUMBER= 1
UNIT_CELL_CONSTANTS= 38.3 79.1 79.1 90 90 90
OUTPUT_FILE=temp.ahkl
SAVE_CORRECTION_IMAGES=FALSE
FRIEDEL'S_LAW=TRUE
eof
find $PWD/../wedge* -name XDS_ASCII.HKL | awk '{print "INPUT_FILE=",$0;print "NBATCH=1 CORRECTIONS=DECAY"}' >> XSCALE.INP
</pre>
<pre>
<pre>
  SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
  SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
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yields a iso.pdb which is far from a single cluster; it is a severely elongated single cloud. We must now investigate whether the data have lower than tetragonal symmetry.
yields a iso.pdb which is far from a single cluster; it is a severely elongated single cloud. We must now investigate whether the data have lower than tetragonal symmetry.
XSCALEing with
XSCALEing with
  SPACE_GROUP_NUMBER=19
  SPACE_GROUP_NUMBER=16
  UNIT_CELL_CONSTANTS=38.3 79.1 79.1 90 90 90
  UNIT_CELL_CONSTANTS=38.3 79.1 79.1 90 90 90
gives a new temp.ahkl, with orthorhombic symmetry.
gives a new temp.ahkl, with orthorhombic symmetry.
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     1.80        7927    1570      1701      92.3%    104.8%    225.2%    7811    0.70    116.1%    42.6*    -5    0.425    785
     1.80        7927    1570      1701      92.3%    104.8%    225.2%    7811    0.70    116.1%    42.6*    -5    0.425    785
     total      130885  22874    23173      98.7%      38.3%    41.0%  130103    2.77    42.1%    92.0*    3    0.703  13546
     total      130885  22874    23173      98.7%      38.3%    41.0%  130103    2.77    42.1%    92.0*    3    0.703  13546
At this point, we run
xdscc12 -w XSCALE.1.HKL | grep ^a | sort -nk6
and find that data sets 1 and 17 are wrongly included in the cloud of 51 data sets. Thus they are removed manually from XSCALE.INP.
We then re-run XSCALE with MERGE=TRUE. The resulting XSCALE.1.HKL is then used as REFERENCE_DATA_SET for a second round of integration with XDS.
pointless xdsin XSCALE.1.HKL
gives
<pre>
  Spacegroup        TotProb SysAbsProb    Reindex        Conditions
    P 21 21 21 ( 19)    0.896  0.924                        h00: h=2n, 0k0: k=2n, 00l: l=2n (zones 1,2,3)
    ..........
    P 2 21 21 ( 18)    0.044  0.045                        0k0: k=2n, 00l: l=2n (zones 2,3)
    ..........
    P 21 21 2 ( 18)    0.015  0.015                        h00: h=2n, 0k0: k=2n (zones 1,2)
    ..........
    P 21 2 21 ( 18)    0.014  0.014                        h00: h=2n, 00l: l=2n (zones 1,3)
---------------------------------------------------------------
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) =    0.87
Laue group confidence  (= Sqrt(Score * (Score - NextBestScore))) =    0.97
Selecting space group P 21 21 21 as there is a single space group with the highest score
<!--SUMMARY_BEGIN--> $TEXT:Result: $$ $$
Best Solution:    space group P 21 21 21
  Reindex operator:                  [h,k,l]               
  Laue group probability:            0.970
  Systematic absence probability:    0.924
  Total probability:                  0.896
  Space group confidence:            0.874
  Laue group confidence              0.966
  Unit cell:  38.30  79.10  79.10    90.00  90.00  90.00
  79.10 to  2.47  - Resolution range used for Laue group search
  79.10 to  1.80  - Resolution range in file, used for systematic absence check
</pre>
== Round 2: using the REFERENCE_DATA_SET ==
The processing script integrate.rc is changed a bit:
#!/bin/bash -f
for f in `seq 1 100`;
do
export OUT=wedge0`printf "%03d" $f`
export NAMES="$PWD/Illuin/microfocus/xtal"`printf "%03d" $f`"_1_00\?.img"
rm -rf $OUT
mkdir $OUT
cd $OUT
generate_XDS.INP $NAMES
echo REFERENCE_DATA_SET=../reference.hkl >> XDS.INP
echo MINIMUM_I/SIGMA=50 >>XDS.INP
sed -i s"/SPOT_RANGE=1 1/SPOT_RANGE=1 3/" XDS.INP
sed -i s"/SPACE_GROUP_NUMBER=0/SPACE_GROUP_NUMBER=19/" XDS.INP
sed -i s"/UNIT_CELL_CONSTANTS= 70 80 90/UNIT_CELL_CONSTANTS=38.3 79.1 79.1/" XDS.INP
sed -i s"/TRUSTED_REGION=0.0 1.2/TRUSTED_REGION=0 1/" XDS.INP
sed -i s"/INCLUDE_RESOLUTION_RANGE=50 0/INCLUDE_RESOLUTION_RANGE=99 1.8/" XDS.INP
/usr/local/bin/xds_par
cd ..
done
mkdir xscale
cd xscale
cat >XSCALE.INP <<eof
SPACE_GROUP_NUMBER= 19
UNIT_CELL_CONSTANTS= 38.3 79.1 79.1 90 90 90
OUTPUT_FILE=temp.ahkl
SAVE_CORRECTION_IMAGES=FALSE
eof
find $PWD/../wedge* -name XDS_ASCII.HKL | awk '{print "INPUT_FILE=",$0;print "NBATCH=3 CORRECTIONS=ALL"}' >> XSCALE.INP
and we get as XSCALE.LP :
<pre>
      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  CC(1/2)  Anomal  SigAno  Nano
  LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
    8.04        2960    473      476      99.4%      6.2%      5.5%    2955  29.90      6.7%    99.8*    86*  2.824    166
    5.68        5486    890      894      99.6%      4.9%      5.9%    5478  27.38      5.3%    99.7*    86*  2.384    363
    4.64        6934    1136      1138      99.8%      4.9%      5.8%    6918  27.64      5.4%    99.8*    76*  1.829    480
    4.02        8066    1363      1367      99.7%      5.3%      5.9%    8045  26.67      5.9%    99.6*    57*  1.426    590
    3.59        9121    1535      1539      99.7%      6.1%      6.3%    9092  25.58      6.7%    99.6*    50*  1.298    666
    3.28      10222    1690      1694      99.8%      6.8%      6.8%    10203  24.69      7.5%    99.4*    36*  1.204    751
    3.04      10990    1831      1834      99.8%      8.5%      8.0%    10970  21.40      9.3%    99.3*    22*  1.086    827
    2.84      12065    1993      1999      99.7%      11.2%    11.1%    12038  17.68    12.2%    99.0*    24*  1.085    894
    2.68      12771    2120      2124      99.8%      14.7%    15.1%    12738  14.78    16.1%    98.4*    14*  0.960    952
    2.54      13054    2196      2198      99.9%      18.9%    20.2%    13026  12.53    20.8%    97.7*    13*  0.867    995
    2.42      14290    2372      2375      99.9%      24.9%    27.1%    14261  10.34    27.3%    96.1*    6    0.813    1083
    2.32      14704    2432      2438      99.8%      29.8%    32.5%    14676    9.21    32.6%    95.1*    8    0.843    1115
    2.23      15623    2582      2593      99.6%      33.0%    35.0%    15587    8.83    36.1%    93.0*    6    0.831    1180
    2.15      15732    2610      2613      99.9%      37.1%    39.2%    15697    8.10    40.6%    91.0*    8    0.818    1203
    2.08      16782    2788      2795      99.7%      44.1%    47.0%    16741    7.01    48.3%    88.3*    4    0.797    1276
    2.01      16783    2802      2809      99.8%      46.8%    48.7%    16747    6.54    51.2%    89.5*    3    0.807    1293
    1.95      18262    3043      3051      99.7%      56.5%    58.0%    18221    5.61    61.9%    85.9*    0    0.803    1402
    1.89      17810    2979      2988      99.7%      68.3%    69.8%    17769    4.63    74.8%    80.0*    7    0.864    1374
    1.84      18503    3112      3117      99.8%      87.5%    90.3%    18454    3.55    96.0%    69.6*    3    0.838    1435
    1.80      16130    2988      3185      93.8%    101.2%    110.5%    15959    2.77    111.7%    62.9*    2    0.798    1276
    total      256288  42935    43227      99.3%      13.4%    14.0%  255575  11.63    14.6%    99.6*    21*  0.975  19321
</pre>
The structure can now easily be solved with hkl2map:
Kay
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