Tough Spots ACA2014

From XDSwiki

There are only 10 frames (numbered 140-149, [1]) available to the public at the time of the ACA2014, so we'll see what we can learn from these.

After starting XDSGUI, we go the "Frames" tab and load frame 140. We then move the mouse to the place where the beam stop position is (1584, 1542) because the header values are obviously wrong. These values are then entered into the XDS.INP tab to have

ORGX= 1584.0 ORGY= 1542.0 

and adjust

DATA_RANGE=140 149
SPOT_RANGE=140 149

because generate_XDS.INP (which is a script that XDSGUI uses) assumes that frame numbers start at 1. We then "Save" and "Run XDS".

Unfortunately (but not quite unexpectedly, given the poor data), IDXREF stops with an the message:

!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS
AUTOMATIC DATA PROCESSING STOPPED. AS THE CRITERIA FOR A GOOD
SOLUTION ARE RATHER STRICT, YOU MAY CHOOSE TO CONTINUE DATA
PROCESSING AFTER CHANGING THE "JOB="-CARD IN "XDS.INP" TO
"JOB= DEFPIX INTEGRATE CORRECT".
IF THE BEST SOLUTION IS REALLY NONSENSE YOU SHOULD FIRST HAVE
A LOOK AT THE ASCII-FILE "SPOT.XDS". THIS FILE CONTAINS THE
INITIAL SPOT LIST SORTED IN DECREASING SPOT INTENSITY. SPOTS
NEAR THE END OF THE FILE MAY BE ARTEFACTS THAT CAN BE ERASED.
ALTERNATIVELY YOU MAY TRY DIFFERENT VALUES FOR "INDEX_ORIGIN"
AS SUGGESTED IN THE ABOVE LISTING.
IF THE CRYSTAL HAS SLIPPED AT THE BEGINNING OF DATA COLLECTION
YOU MAY CHOOSE TO SKIP SOME OF THE FIRST FRAMES BY CHANGING 
THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.

Upon inspection of IDXREF.LP, we find

  #  COORDINATES OF REC. BASIS VECTOR    LENGTH   1/LENGTH

   1  -0.0074106-0.0078746-0.0096180  0.0144717      69.10
   2   0.0161275-0.0177932 0.0018581  0.0240862      41.52
   3  -0.0063143-0.0049258 0.0088081  0.0119045      84.00

CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS 

  #  COORDINATES OF VECTOR CLUSTER   FREQUENCY       CLUSTER INDICES   
   1 -0.0160472 0.0177317-0.0019319      437.      0.00     -1.00     -0.01
   2 -0.0137156-0.0127408-0.0007731      375.      1.00     -0.00      1.00
   3 -0.0297229 0.0049461-0.0025837      345.      0.99     -0.99      1.00
   4 -0.0023894 0.0305421-0.0010979      344.     -1.00     -1.00     -1.00
   5  0.0321961-0.0355153 0.0038075      320.     -0.00      2.00      0.01
   6 -0.0087489 0.0256212 0.0075593      268.     -0.99     -1.00     -0.01
   7  0.0074386 0.0078204 0.0094374      256.     -0.99      0.00     -0.01
   8  0.0223977-0.0127581-0.0067617      251.     -0.01      1.00     -0.99
   9  0.0459042-0.0228053 0.0045272      250.     -1.00      2.00     -1.00
  10  0.0248981-0.0434002-0.0058534      247.      0.99      2.00     -0.00
  11 -0.0184690 0.0482571-0.0029946      242.     -0.99     -1.99     -1.00
  12  0.0235478-0.0099933 0.0113274      240.     -0.99      1.00     -0.01
  13  0.0385187-0.0305663-0.0049896      237.     -0.01      2.00     -0.99
  14 -0.0063089-0.0049976 0.0085815      229.      0.01      0.00      0.99
  15  0.0396875-0.0277897 0.0131522      225.     -0.99      2.00     -0.01
  ...

So all the difference vectors are integral, which gives us confidence into the primitive cell parameters, listed below the table:

PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
    41.52     69.10     84.01     90.28     90.43     90.45

Is it a single lattice?

SUBTREE    POPULATION

    1         1220
    2           33
    3            7
    4            4
   ...

Well, almost all (1220) reflections do belong to the prominent lattice.

Next, the program tests alternative origins:

XD,YD    computed direct beam position (pixels) on detector 
         given beam position (pixel):  1584.00  1542.00
X,Y,Z    computed coordinates of the direct beam wave vector
DH,DK,DL mean absolute difference between observed and 
         fitted indices

 INDEX_   QUALITY  DELTA    XD       YD       X       Y       Z       DH      DK      DL
 ORIGIN

 0  0  0      2.8    0.4   1572.6   1549.6 -0.0056  0.0037  0.9992    0.23    0.04    0.05
 0  0 -1      7.4    0.5   1585.6   1560.7  0.0008  0.0091  0.9992    0.23    0.43    0.55
 0 -1  0      9.4    0.6   1587.8   1564.7  0.0018  0.0111  0.9992    0.23    0.46    0.58
 0  0  1      9.4    0.7   1559.8   1538.8 -0.0118 -0.0016  0.9992    0.23    0.39    0.50
 0 -1  1     11.6    0.4   1575.0   1553.8 -0.0044  0.0058  0.9992    0.23    0.87    1.10
 0  1 -1     12.1    0.4   1570.1   1545.3 -0.0068  0.0016  0.9992    0.23    0.90    1.16
 0  1  0     12.3    0.8   1557.1   1534.2 -0.0131 -0.0038  0.9991    0.23    0.49    0.64
 1  0  0     13.8    1.0   1605.7   1513.0  0.0106 -0.0141  0.9991    0.23    0.05    0.06
 0 -1 -1     15.0    1.1   1600.7   1575.8  0.0082  0.0164  0.9991    0.23    0.06    0.07
 ...

and based on the given origin, the QUALITY is best and the deviations DH, DK, DL are small - at least for DK and DL, whereas the reflections are smeared along the short axis.

Next, the possible Bravais lattices are tested for consistence with the primitive cell:

 LATTICE-  BRAVAIS-   QUALITY  UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
CHARACTER  LATTICE     OF FIT      a      b      c   alpha  beta gamma

*  44        aP          0.0      41.8   68.9   84.1  90.0  91.1  91.6
*  31        aP          1.3      41.8   68.9   84.1  90.0  88.9  88.4
*  34        mP         20.7      41.8   84.1   68.9  90.0  91.6  91.1
*  33        mP         24.1      41.8   68.9   84.1  90.0  91.1  91.6
*  35        mP         42.2      68.9   41.8   84.1  91.1  90.0  91.6
*  32        oP         43.5      41.8   68.9   84.1  90.0  91.1  91.6
   29        mC        239.6      41.8  142.9   84.1  90.4  91.1  74.6
   28        mC        244.6      41.8  172.4   68.9  90.4  91.6  77.1
...

Good "Quality of fit" values (0 to 1) are only obtained for P1 ("aP"), and medium-quality (around 20) for two different settings of P2(1) ("mP"), namely those with the middle and the long axis as unique axes. If the short axis were considered the unique axis, the "Quality of fit" is significantly worse (43.5) so this is not an option. Thus, we've narrowed down the space group possibilities; only three are left.

INTEGRATE and CORRECT

To continue after the error message printed by IDXREF, we change XDS.INP to have

JOB= DEFPIX INTEGRATE CORRECT

and then "Save" and "Run XDS".

The program happily integrates

IMAGE IER  SCALE     NBKG NOVL NEWALD NSTRONG  NREJ  SIGMAB  SIGMAR
  140   0  1.003  8573222    0   5737     187    18  0.1577  0.2374
  141   0  1.009  8575812    0   5755     175     7  0.1714  0.2758
  142   0  1.008  8584295    0   5754     172     9  0.1604  0.2698
  143   0  1.015  8580937    0   5710     160    15  0.1743  0.2532
  144   0  1.012  8584356    0   5736     178    12  0.1553  0.2576
  145   0  1.012  8588220    0   5760     184    18  0.1676  0.2299
  146   0  1.015  8584920    0   5762     151    11  0.1732  0.2858
  147   0  1.016  8586552    0   5774     154    13  0.1778  0.3305
  148   0  1.017  8583396    0   5765     178    11  0.1638  0.3394
  149   0  1.015  8586598    0   5811     154     9  0.1684  0.3231

and then goes to the CORRECT stage.

Unfortunately, the automatic space group determination is difficult, because there are too few symmetry-related reflections.

SPACE-GROUP         UNIT CELL CONSTANTS            UNIQUE   Rmeas  COMPARED  LATTICE-
  NUMBER      a      b      c   alpha beta gamma                            CHARACTER
      1      41.9   68.7   84.0  90.2  89.0  88.5     182     0.0        0    31 aP
     16      41.9   68.7   84.0  90.0  90.0  90.0     165    72.5       17    32 oP
      3      68.7   41.9   84.0  90.0  90.2  90.0     168    70.8       14    35 mP
      3      41.9   68.7   84.0  90.0  91.0  90.0     180   136.1        2    33 mP
      3      41.9   84.0   68.7  90.0  91.5  90.0     181     0.0        1    34 mP
      1      41.9   68.7   84.0  90.2  91.0  91.5     182     0.0        0    44 aP

It may be interesting to look at the predicted reflection positions at this stage. So we move to the TOOLS tab and run "Show frame with predicted spots" for frame 140. This gives

Click for larger image

The agreement between actual and predicted spots is reasonably good.

At this point, we cannot continue without more information.