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Solve a small-molecule structure (edit)

Revision as of 21:52, 28 February 2011

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(Created page with "The following is based on the experience of a protein crystallographer who one day obtained a small-molecule dataset and managed to solve and refine it without prior knowledge wh...")
 
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  OUTPUT_FILE=temp.hkl
  OUTPUT_FILE=temp.hkl


== run [[XPREP]] to find out the spacegroup ==
== first try: wrong spacegroup ==
=== run [[XPREP]] to find out possible spacegroups ===
answer the question concerning the cell axes, and then hit <Enter> several times until the program suggests a list of spacegroups - this choice is going to be important. It helps a bit to observe earlier whether it's centrosymmetric or not, from the line: Mean |E*E-1| = 0.939 [expected .968 centrosym and .736 non-centrosym].  
answer the question concerning the cell axes, and then hit <Enter> several times until the program suggests a list of spacegroups - this choice is going to be important. It helps a bit to observe earlier whether it's centrosymmetric or not, from the line: Mean |E*E-1| = 0.939 [expected .968 centrosym and .736 non-centrosym].  
<pre>
Systematic absence exceptions:
        b--  c--  n--  21--  -c-  -a-  -n-  -21-  --a  --b  --n  --21
N      938  938    0    0  411    0  411    0    0  237  237    0
N I>3s  706  706    0    0  304    0  304    0    0  203  203    0
<I>    50.0  50.0  0.0  0.0  43.1  0.0  43.1  0.0  0.0  56.6  56.6  0.0
<I/s>  14.1  14.1  0.0  0.0  15.2  0.0  15.2  0.0  0.0  16.4  16.4  0.0
Identical indices and Friedel opposites combined before calculating R(sym)
Option  Space Group  No.  Type  Axes  CSD  R(sym) N(eq)  Syst. Abs.  CFOM
[A] P222          # 16  chiral  1    14  0.022  9725  0.0 / 10.7  11.72
[B] Pmm2          # 25  non-cen  1    9  0.022  9725  0.0 / 10.7  15.05
[C] Pmm2          # 25  non-cen  5    9  0.022  9725  0.0 / 10.7  15.05
[D] Pmm2          # 25  non-cen  3    9  0.022  9725  0.0 / 10.7  15.05
[E] Pmmm          # 47  centro  1    7  0.022  9725  0.0 / 10.7  13.52
[F] P222(1)        # 17  chiral  1    26  0.022  9725  0.0 / 10.7  8.76
[G] P222(1)        # 17  chiral  5    26  0.022  9725  0.0 / 10.7  8.76
[H] P222(1)        # 17  chiral  3    26  0.022  9725  0.0 / 10.7  8.76
[I] P2(1)2(1)2    # 18  chiral  1  359  0.022  9725  0.0 / 10.7  5.33
[J] P2(1)2(1)2    # 18  chiral  5  359  0.022  9725  0.0 / 10.7  5.33
[K] P2(1)2(1)2    # 18  chiral  3  359  0.022  9725  0.0 / 10.7  5.33
[L] P2(1)2(1)2(1)  # 19  chiral  1  5917  0.022  9725  0.0 / 10.7  5.07
[M] Pmc2(1)        # 26  non-cen  3    20  0.022  9725  0.0 / 10.7  9.81
[N] Pmc2(1)        # 26  non-cen  4    20  0.022  9725  0.0 / 10.7  9.81
[O] Pmma          # 51  centro  1    14  0.022  9725  0.0 / 10.7  7.69
[P] Pmma          # 51  centro  6    14  0.022  9725  0.0 / 10.7  7.69
[R] Pma2          # 28  non-cen  1    1  0.022  9725  0.0 / 10.7  55.05
[S] Pma2          # 28  non-cen  6    1  0.022  9725  0.0 / 10.7  55.05
[T] Pmn2(1)        # 31  non-cen  2    53  0.022  9725  0.0 / 10.7  6.90
[U] Pmn2(1)        # 31  non-cen  5    53  0.022  9725  0.0 / 10.7  6.90
[V] Pmmn          # 59  centro  3    42  0.022  9725  0.0 / 10.7  3.35
[W] Pcc2          # 27  non-cen  3    2  0.022  9725  0.0 / 10.7  38.39
[X] Pccm          # 49  centro  3    1  0.022  9725  0.0 / 10.7  51.02
[Y] Pna2(1)        # 33  non-cen  1  903  0.022  9725  0.0 / 10.7  5.16
[Z] Pna2(1)        # 33  non-cen  6  903  0.022  9725  0.0 / 10.7  5.16
[0] Pnma          # 62  centro  1  894  0.022  9725  0.0 / 10.7  1.14
[1] Pnma          # 62  centro  6  894  0.022  9725  0.0 / 10.7  1.14
[2] Pccn          # 56  centro  3  196  0.022  9725  0.0 / 10.7  1.53
Option [1] chosen
</pre>
(The program chooses Option "1" (Pnma) by default, which later turns out to be wrong. How the correct spacegroup (Pccn) could be identified at this point, I don't know.)
After that, say "c" for "define unit-cell CONTENTS", and input a reasonable number of carbon atoms (I used C20). Get out of this menu with "E". Then, choose "f" for "set up shelxtl FILES". Then, answer the question "XM/SHELXD (M) or XS/SHELXS (S) format [S]:" with "m" since we're going to use shelxd for solving the structure. Answer the question about the name (I used the spacegroup number as I knew I would have to test several possibilities). Finally, "q"uit the program. The resulting 62.ins is:
After that, say "c" for "define unit-cell CONTENTS", and input a reasonable number of carbon atoms (I used C20). Get out of this menu with "E". Then, choose "f" for "set up shelxtl FILES". Then, answer the question "XM/SHELXD (M) or XS/SHELXS (S) format [S]:" with "m" since we're going to use shelxd for solving the structure. Answer the question about the name (I used the spacegroup number as I knew I would have to test several possibilities). Finally, "q"uit the program. The resulting 62.ins is:
  TITL 62 in Pnma  
  TITL 62 in Pnma  
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  END
  END


== solving the structure with [[SHELX C/D/E|SHELXD]] ==
=== solving the structure with [[SHELX C/D/E|SHELXD]] ===
Just run "shelxd 62". You may interrupt it with Ctrl-C once it has found good solutions, as evidenced by
Just run "shelxd 62". You may interrupt it with Ctrl-C once it has found good solutions, as evidenced by
  Try 68:20  Peaks 99 96 71 68 63 55 53 51 50 48 46 45 45 44 44 43 43 43 41 40
  Try 68:20  Peaks 99 96 71 68 63 55 53 51 50 48 46 45 45 44 44 43 43 43 41 40
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C005  1  0.84406  0.88664  0.13204 11.00000 0.1  61.71
C005  1  0.84406  0.88664  0.13204 11.00000 0.1  61.71
C006  1  0.23705  0.75000 -0.14287 10.50000 0.1  61.63
C006  1  0.23705  0.75000 -0.14287 10.50000 0.1  61.63
C007  1  0.71260  0.88327  0.09698 11.00000 0.1  60.92
...
C008  1  0.65969  0.78420 -0.13163 11.00000 0.1  59.90
C009  1  0.33293  0.91881 -0.04193 11.00000 0.1  58.80
C010  1  0.84248  0.99455 -0.16293 11.00000 0.1  58.58
C011  1  0.33883  0.78497 -0.20937 11.00000 0.1  56.06
C012  1  0.78396  0.94630  0.02080 11.00000 0.1  55.98
C013  1  0.97651  0.99845 -0.10805 11.00000 0.1  55.35
C014  1  0.90340  0.82762 -0.12071 11.00000 0.1  55.25
C015  1  0.16673  0.90700  0.07074 11.00000 0.1  55.25
C016  1  0.71552  0.97497 -0.17793 11.00000 0.1  54.99
C017  1  0.77400  0.78674 -0.00654 11.00000 0.1  54.97
C018  1  0.18750  0.90013 -0.13125 11.00000 0.1  54.86
C019  1  0.43404  0.85828  0.15317 11.00000 0.1  54.85
C020  1  0.51732  0.82874  0.09415 11.00000 0.1  54.52
C021  1  0.99843  0.84427 -0.05892 11.00000 0.1  54.40
C022  1  0.64265  0.91301  0.04166 11.00000 0.1  54.11
C023  1  0.18994  0.90304 -0.02101 11.00000 0.1  53.98
C024  1 -0.00029  0.87744 -0.23364 11.00000 0.1  53.75
C025  1  0.30272  0.89035  0.02043 11.00000 0.1  53.54
C026  1  0.72766  0.95461 -0.10200 11.00000 0.1  51.40
C026  1  0.72766  0.95461 -0.10200 11.00000 0.1  51.40
C027  1  0.77380  0.96500  0.10122 11.00000 0.1  49.11
C027  1  0.77380  0.96500  0.10122 11.00000 0.1  49.11
Line 94: Line 125:
</pre>
</pre>


== Refinement in [[SHELXL]] ==
=== Refinement in [[SHELXL]] ===
It makes sense to remove the last 4 atoms since their occupancy is less than 25%, and the final remaining atom then is at 49% - a large jump.
In this example, it makes sense to remove the last 4 atoms since their occupancy is less than 25% of the maximum, and the final remaining atom then is at 49% - a large jump.
Insert
Insert
  ACTA
  ACTA
  LIST 6
  LIST 6
  L.S. 10
  L.S. 10
after the UNIT 220 instruction, and run shelxl 62.
after the UNIT 220 instruction, and run "shelxl 62".
 
It turns out that the R-factor does not really go down properly, and this means that the spacegroup is wrong. The "FINAL CC 58.70" result from SHELXD is probably also suspiciously low, I guess.
Kay
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