X-Ray Crystallography

Extras

Checklist

Check ADPs for high/low/NPD values.
Relabel atoms to final values and sort before adding Hs.
If chiral with a high sd of the Flack parameter,merge the Friedel pairs(MERG 4 in SHELX)
Run checkCIF.

Fragments

FRAG 17 1.57 1.57 1.57 90 90 90
#PF6
P1 0.0 0.0 0.0
F1 0.0 -1.0 0.0
F2 1.0 0.0 0.0
F3 0.0 1.0 0.0
F4 -1.0 0.0 0.0
F5 0.0 0.0 -1.0
F6 0.0 0.0 1.0
FEND
FRAG 17 6.1269 14.6159 12.6541 90 103.228 90 (ACERAC)
# (CH3)2NC=O:(Dimethyl Formamide DMF)
C8 1 0.096400 0.094890 0.319840 1.000000 0.05000
O3 4 -0.087730 0.060150 0.321010 1.000000 0.05000 #cis to C9
N1 3 0.175730 0.103760 0.231480 1.000000 0.05000
C9 1 0.048500 0.072200 0.126620 1.000000 0.05000
C10 1 0.392900 0.145430 0.234700 1.000000 0.05000
FEND
#(CH3)2C=O:acetone
FRAG 17 7.884 10.5648 24.6438 90 90 90 (ABEGUK)
O7 4 0.495600 0.811900 0.176790 1.000000 0.05000
C19 1 0.467300 0.876600 0.216690 1.000000 0.05000
C20 1 0.550400 1.002600 0.223430 1.000000 0.05000
C21 1 0.349200 0.834100 0.260300 1.000000 0.05000
FEND
#!CH3NO2
FRAG 17 10.331 6.322 8.52 90 90 90 (ADEZUF)
C2 1 0.809000 0.861000 0.714600 1.000000 0.05000
N1 3 0.813600 0.710300 0.579300 1.000000 0.05000
O1 4 0.887600 0.748200 0.472500 1.000000 0.05000
O2 4 0.742800 0.556800 0.582800 1.000000 0.05000
FEND
#!CCL2
FRAG 17 7.9711 8.3909 9.5169 99.1945 108.748 110.617 (ACIWOY)
C22 1 0.654200 -0.205400 -0.443100 1.000000 0.05000
Cl1 5 0.718700 -0.366390 -0.377580 1.000000 0.05000
Cl2 5 0.457300 -0.303900 -0.626600 1.000000 0.05000
FEND
#!Et2O
FRAG 17 16.648 17.329 27.222 90 101.753 90 (BEMJOT)
C81 1 0.537600 0.525800 0.196670 1.000000 0.05000
C82 1 0.548800 0.518900 0.252330 1.000000 0.05000
C83 1 0.475800 0.519900 0.317730 1.000000 0.05000
C84 1 0.393000 0.539300 0.328930 1.000000 0.05000
O13 4 0.471940 0.530420 0.265750 1.000000 0.05000
FEND
#!MeCN Need at least three atoms but what if one is zero occupancy?
FRAG 17 13.489 28.657 15.063 90 116.552 90
C53 1 -0.848800 1.328150 -0.307500 1.000000 0.05000
C54 1 -0.756600 1.333230 -0.331200 1.000000 0.05000
N9 3 -0.684500 1.337600 -0.349900 1.000000 0.05000
FEND
#Pivolate->acetate as Mes position is uncertain(CEBZEP)
FRAG 17 11.0624 16.4631 15.3066 90 92.591 90
O1 3 0.136590 0.153720 0.322840 1.000000 0.05000
O2 3 0.131980 0.131600 0.463340 1.000000 0.05000
C1 1 0.185030 0.123740 0.392660 1.000000 0.05000
C2 1 0.305400 0.078190 0.391400 1.000000 0.05000
# Mes
C3 1 0.367900 0.096100 0.308600 1.000000 0.05000
C4 1 0.381500 0.100900 0.473100 1.000000 0.05000
C5 1 0.276700 -0.013000 0.396800 1.000000 0.05000
FEND
# tert-butyl: C1 bonds to rest of moiety. Coors set so z is bond length;1.54 is default for all
FRAG 17 1 1 1 90 90 90
C1 1 0. 0. 1.54
# centre
C2 1 0. 0. 0.
#base (x,0,-r) (-d,+-a/2,-r):x=2sqrt(2)R/3,a=4R/(6)**1/2,d=(2**1/2)*R/3,r=R/3
,R=1.54
C3 1 1.452 0. -0.513
C4 1 -0.726 1.257 -0.513
C5 1 -0.726 -1.257 -0.513
FEND
##################### FRAG #... FEND then AFIX # then AFIX 6 rigid body;AFIX Hs can be
added; AFIX 5 to mark dependent atoms afterwards.See s2932
E.g.
FRAG 17 10.331 6.322 8.52 90 90 90
C73 1 0.809000 0.861000 0.714600 11.000000 0.050000
N1 7 0.813600 0.710300 0.579300 11.000000 0.050000
O3 3 0.887600 0.748200 0.472500 11.000000 0.050000
O4 3 0.742800 0.556800 0.582800 11.000000 0.050000
FEND
PART 2 -21
AFIX 176
C73S 1 0.832023 0.191839 0.487318 -21.00000 0.03545
N1S 7 0.936135 0.264423 0.470437 -21.00000 0.03084
O3S 3 0.938637 0.305853 0.406598 -21.00000 0.05417
O4S 3 1.013437 0.278424 0.521581 -21.00000 0.05721
PART 0
AFIX 0
FRAG 18 7.9711 8.3909 9.5169 99.1945 108.748 110.617
C22 1 0.654200 -0.205400 -0.443100 11.000000 0.05000
Cl1 8 0.718700 -0.366390 -0.377580 11.000000 0.05000
Cl2 8 0.457300 -0.303900 -0.626600 11.000000 0.05000
FEND
PART 1 21
AFIX 186
C73 1 0.847481 0.233581 0.464428 21.00000 0.10272
CL1 8 0.962729 0.222324 0.535778 21.00000 0.05532
CL2 8 0.902124 0.294548 0.380703 21.00000 0.03877
PART 0
AFIX 0

Relabel Hs so unique and no longer than 4 characters

# Renumber Hs so #=>100 fit in 4 characters
gawk 'BEGIN{split("Z,Y,X,W,V,U,T,S,R,Q,P,O,N,M,L,K,J,I",lab,",");nm=0};\
!/^H[0-9][0-9][0-9]/{nm=0;print};/^H[0-9][0-9][0-9]/{a=$1;\
$1="H"substr(a,3,2)lab[substr(a,2,1)*3-nm];print;nm++}' old.res>new.res

SHELXTL & Vista

Right-click on Desktop

Click 'Personalize'

Click 'Windows Color and Appearance'

Click 'Open classic appearance properties for more color options'

Choose 'Windows Standard' and click 'Apply' and 'OK'

Twinning_&_CheckCIF

George M. Sheldrick:

Use the current (2008/4) version of TWINABS. ALWAYS merge the data when writing the HKLF 5 file with TWINABS, because it is not possible to merge these data later (e.g. in XL/SHELXL). Merging groups of equivalents containing different components is a non-trivial exercise and is best done by TWINABS. Note that if (as here) there are more 'observations' that there are 'unique reflections', to get the correct esds you need to set the third number on the L.S. instruction to the difference of these two numbers (they can be found at the end of the summary that is output to the console). You also need to explain to the Editor that you have done this and that he should ignore the corresponding CheckCIF warning.

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