DirAx Course

This course will show you the input and output for the examples 0 and 5. Example 0 is a straighforward run. Example 5 shows how to find multiple lattices.

A full run of example 0.

Note, the bold text is typed by you.
dirax

Dirax version 1.09b, 22-Feb-1999 C O N D I T I O N S F O R U S E ===================================== a. You may not copy DirAx neither the auxiliary files except for use by yourself or for use in your laboratory, institute, office and the like. b. You may not hand over DirAx in any form to third parties without provable permission from the author. c. You use DirAx at your own responsibility completely. Albert J.M. Duisenberg, Antoine M.M. Schreurs BIJVOET Centre for Biomolecular Research Laboratory for Crystal and Structural Chemistry Utrecht University since A.D. MDCXXXVI Padualaan 8, NL-3584 CH UTRECHT The Netherlands Electronic MAIL adresses: a.j.m.duisenberg@chem.uu.nl, a.m.m.schreurs@chem.uu.nl Indexfit:2.0 Levelfit:1/1000 Dmax:80 shortacl=false AxisZero:0.05 AngleZero:0.1 CompareAxis:1.0 CompareAngle:5.0 CompareFactor:20.0 CorrelateRatio:10.0
Dirax> example 0

ex00 - This is a straightforward model run for a single lattice. (In fact too easy for DirAx.) go ! run with defaults lo ! accept proposed ACL and show H indices ro ! show cell and [R] and [D] matrices write ! write file ex00.out for print-out 25 reflections from file /mnt/ccd/p/dirax/ex00.drx
Dirax> go

2600 triplets 2600 final triplets 2570 triplet vectors Squishd: 2570 t vectors ==> 1922 t vectors Sorting 1922 t vectors... Reducing 1922 t vectors ==> 805 t vectors Acl #H a b c alpha beta gamma Volume Indexstatus 25 25 6.530 41.209 6.671 89.99 101.53 90.00 1759 HHHHHHHHHHHHHHHHHHHHHHHHH 13 13 6.530 6.671 10.431 88.22 80.99 78.48 440 HnHHnnHnHnHnnHHnHnHHnnnHH 9 9 6.530 6.671 8.410 97.33 97.10 101.54 352 ?nHHnnnnnnHnnHHnHnnnnHnnHH 8 8 5.893 6.519 6.529 116.29 113.09 95.59 195 nnnnHnnnHHHnnnnHHnHnHnnnn 7 7 4.930 5.173 6.530 91.48 104.10 97.39 160 ?HnnnnnnHnnnHHnnnnnnnnHnHH selected ACL 25
Here you see 5 possible solutions. The solutions are identified by the Acl number in the first column. The second column, marked #H, gives the number of fitting reflections. In the last column, marked Indexstatus, the 'fitting' of all the reflections is displayed (H=fit, n=nonfit). The question marks in solutions 9 and 7 indicate some warning. More about this later.
The last line of the output shows the selected solution.
Dirax> lo
nr H K L 1/err dth dom dch Netint H 1: 0.000 16.000 1.000 89052 0.000 0.000 -0.001 130.8 H 2: 2.000 -2.999 1.000 22261 0.001 0.004 0.005 112.3 H 3: 0.000 -15.999 1.000 14127 -0.002 0.007 -0.003 141.7 H 4: 0.000 -12.002 1.000 26078 0.001 0.001 -0.004 194.5 H 5: -1.000 -5.001 2.001 6090 0.007 0.001 0.008 99.2 H 6: -1.000 -4.001 2.000 28873 0.000 0.001 -0.006 82.0 H 7: -1.000 5.001 2.000 15203 -0.002 -0.006 -0.006 87.8 H 8: 0.000 -16.998 1.000 21427 -0.002 0.003 0.001 144.1 H 9: -1.000 8.997 1.000 11459 -0.003 -0.001 0.009 173.0 H 10: 1.000 8.000 1.000 34777 0.001 -0.001 0.004 69.6 H 11: 2.000 -2.000 1.999 8708 -0.005 -0.002 -0.002 141.3 H 12: 1.000 4.002 1.001 7714 0.006 0.005 0.003 43.4 H 13: -1.000 -4.998 1.000 9340 -0.005 0.000 0.002 334.6 H 14: -0.999 4.998 1.000 9967 -0.004 -0.003 0.002 332.7 H 15: -1.000 9.001 0.000 12960 0.000 -0.013 -0.010 148.9 H 16: -1.000 -4.002 0.000 14346 0.003 0.003 -0.007 330.6 H 17: -1.000 5.004 0.000 8954 0.003 -0.024 -0.011 197.6 H 18: 1.000 -4.001 0.000 15309 0.002 0.003 -0.012 371.0 H 19: 1.000 -5.001 0.000 14639 0.003 0.006 0.001 178.5 H 20: -1.000 1.000 1.001 8374 0.005 0.001 0.010 1537.2 H 21: -1.000 0.000 1.000 21252 0.002 0.003 -0.003 1100.8 H 22: 1.000 -2.000 2.000 17431 -0.003 0.000 -0.002 62.5 H 23: -1.000 2.000 0.000 12613 -0.002 -0.008 -0.019 304.3 H 24: -1.000 1.001 0.000 19948 0.002 -0.006 -0.008 579.3 H 25: 1.000 -1.001 0.000 17501 0.002 -0.006 -0.012 532.3 1/error for H: from 6090 to 89052.

Column 1: H (=fit) or n (=nonfit).
There are no n's in this example.
Column 2: reflection number
Columns 3 to 5: reflection indices.
The indices are presented as floating numbers.
Column 6: 1/error.
There are 2 c-vectors: c_obs, the observed c-vector, and c_calc, the calculated c-vector with all indices rounded to integer. error is defined as the length of the difference vector between c_obs and c_calc. The reciprocal value of error is given in the table. N.B.: a reflection is considered to 'fit' if 1/error > indexfit*levelfit.
Columns 7 to 9: angle differences
These angles are calculated for the Bisecting geometry.
Column 10: reflections intensity

Dirax: write

Created ex00.out

Dirax> end

dirax ended at 23-Jul-1999 15:34:16 CPU time used 00:00:01

The question marks in the Acl solution list mark some warning. In this example, you could select a different solution:
Dirax> acl

Acl  #H    a       b       c     alpha   beta  gamma  Volume  Indexstatus
 25  25   6.530  41.209   6.671  89.99 101.53  90.00    1759  HHHHHHHHHHHHHHHHHHHHHHHHH
 13  13   6.530   6.671  10.431  88.22  80.99  78.48     440  HnHHnnHnHnHnnHHnHnHHnnnHH
  9   9   6.530   6.671   8.410  97.33  97.10 101.54     352 ?nHHnnnnnnHnnHHnHnnnnHnnHH
  8   8   5.893   6.519   6.529 116.29 113.09  95.59     195  nnnnHnnnHHHnnnnHHnHnHnnnn
  7   7   4.930   5.173   6.530  91.48 104.10  97.39     160 ?HnnnnnnHnnnHHnnnnnnnnHnHH

acl/auto [25] 9

selected ACL 9
WARNING: all |K| indices zero or one

Solutions with question marks are not selected as default solution.

A full run of example 5.

Dirax> example 5

ex05 - Data from a twinned crystal. Default parameters. A super solution is found for all reflections, which is common with real twins. Note: It it not possible to give general rules for this sort of problems. The super cell COULD be correct (and IS geometrically!) but you have to consider crystallographical aspects. Here we select ACL 18 because this looks promising. Write results to file ex05.out1. Continue with 'n' (not fitting) reflections only. Now the other lattice is found. Write to file ex05.out2 and compare with .out1 later. Normally with so few 'n' reflections a sub-lattice is found rather then a congruent lattice. Then you have to search further selectively. go ! run with defaults acl 18 ! overrule super lattice solution ACL 25 go ! go again with H-refl's only, for 1st lattice cell ! cell etc. for 1st lattice store a ! save this solution write ex05.out1 ! write file for print-out lch invert ! H -> n and n -> H go ! again with N-refls only, for other lattice loh ! list H refls for 2nd lattice cell ! cell etc. for 2nd lattice store b ! save this solution write ex05.out2 ! write file for print-out compare a b ! compare the two solutions . ! accept proposed solution end The super lattice is geometrically correct, but we know better. The lattices with V=833.7 can be transformed to monoclinic C. NOTE: as usually some reflections fit into both twin lattices. 25 reflections from file /mnt/ccd/p/dirax/ex05.drx
Dirax> go
2600 triplets 2600 final triplets 2564 triplet vectors Squishd: 2564 t vectors ==> 1838 t vectors Sorting 1838 t vectors... Reducing 1838 t vectors ==> 1006 t vectors Acl #H a b c alpha beta gamma Volume Indexstatus 25 25 9.642 15.090 75.029 95.77 93.65 89.98 10839 HHHHHHHHHHHHHHHHHHHHHHHHH 21 21 9.642 15.090 68.772 90.00 91.97 89.97 10000 HHHHHHHHnHnHHHHHHnnHHHHHH 20 20 9.642 15.090 45.886 90.00 91.96 89.98 6672 HnHHHHnnHHHHHHHHHnnHHHHHH 18 18 9.641 9.824 9.827 100.33 105.39 105.35 834 HnHHHHnnnHnHHHHHHnnHHHHHH 7 5 2.345 2.962 7.634 89.12 81.20 84.20 52 ?nnnnHnnnnnnnnnHHnnnnnHnHn selected ACL 25

Solution 25
All reflections fit but the cell volume is much larger than expected.
Solution 21
Four reflections do not fit. The angles alpha and gamma are 90°.
Solution 20
Five reflections do not fit. Also monoclinic angles. Volume much better.
Solution 18
Expected volume. Seven nonfits. The b and c axes are equal, and so are the angles beta and gamma.
Solution 7
Not a real solution.

Dirax> acl 18

selected ACL 18

Now we do another go with the H-reflections only.
Dirax> go

18 H_reflections selected out of 25
969 triplets
969 final triplets
948 triplet vectors
Squishd: 948 t vectors ==> 858 t vectors
Sorting 858 t vectors...
Reducing 858 t vectors ==> 401 t vectors
Acl  #H    a       b       c     alpha   beta  gamma  Volume  Indexstatus
 18  18   9.641   9.824   9.827 100.33 105.39 105.35     834  HnHHHHnnnHnHHHHHHnnHHHHHH
selected ACL 18

Only one solution. Store it.

Dirax> store a

and look for another solution with the nonfits only.

Dirax> lchi

Nfit:7        123456789 123456789 12345
Nonfit:18     nHnnnnHHHnHnnnnnnHHnnnnnn

Dirax> go

7 H_reflections selected out of 25
56 triplets
56 final triplets
56 triplet vectors
Squishd: 56 t vectors ==> 29 t vectors
Sorting 29 t vectors...
Reducing 29 t vectors ==> 27 t vectors
Acl  #H    a       b       c     alpha   beta  gamma  Volume  Indexstatus
  7  10   9.643   9.821   9.826 100.35 105.36 105.34     834  nHnnnnHHHnHnnnnnnHHnnHHHn
selected ACL 7

Another solution, with same volume as the previous one. Store it.

Dirax> store b

Now we want to compare the two solutions.

Dirax> compare a b

Save A :   9.641   9.824   9.827  100.33  105.39  105.35     833.7
HnHHHHnnnHnHHHHHHnnHHHHHH
Save B :   9.643   9.821   9.826  100.35  105.36  105.34     833.6
nHnnnnHHHnHnnnnnnHHnnHHHn
Volume ratio = 1.0 IndexStatus correlation=-0.77
Trying 216 solutions
Nr Rotangle       Rotvec(xyz)           RotVec(hkl)        RotVec(uvw)     Fom
 1 -179.954  0.1913  0.3914  0.9001  11.00 -2.97 -2.97   1.00  0.00  0.00  0.15
 2  179.991  0.7760 -0.6218  0.1055   0.00  1.00  1.00   7.02 12.99 13.00  0.13

First you see the two solutions (cell parameters, volume and index status) The volume ratio is 1.0 (this is ok) and the indexstatus correlation is -0.77. If the index status of both solutions is equal the correlation will be 1.0. If the index status of the two solutions is complementary, the correlation is -1.0. The value here (-0.77) indicates an almost complete complementary relation.
Then there are two solutions. So there are two rotations who map solution a to solution b. The rotation vectors are given in the laboratory system (xyz), in the reciprocal space (hkl) and direct space (uvw). The first solution is a rotation over almost 180 degrees around the a-axis. The second solution is a rotation over almost 180 degrees around the b^*+c^*-diagonal.

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