Chemical Crystallography Laboratory
University of Oxford

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Frequently Asked Questions

Chapter 9: Publication

9.1: An editor wants to know the completeness of the data at 25 degrees

9.2: What's the difference between _theta_max and _theta_full?

9.3: Enantio-pure substance, diagram shows other enantiomer. What to do?

Common problems encountered on trying to submit a paper

Is there a way to get that from CRYSTALS? The current data in the CIF is something like this:

 
  _diffrn_reflns_theta_min              4.123
  _diffrn_reflns_theta_max             28.884 
  _diffrn_measured_fraction_theta_max   0.934 
   
  _diffrn_reflns_theta_full            21.098
  _diffrn_measured_fraction_theta_full  0.996
 

Those pesky editors. Here's what to do:
1) Choose "X-ray data"->"Edit goodies".
2) Locate the box labelled "Theta full (set -ve to fix at absolute value)", and change the value to -25.00
3) Click OK.
4) Make a new CIF.

 _diffrn_reflns_theta_max             28.884 
 _diffrn_measured_fraction_theta_max   0.934 
  
 _diffrn_reflns_theta_full            21.098
 _diffrn_measured_fraction_theta_full  0.996
 

Theta_max is the very highest theta angle found in all of your data. The _diffrn_measured_fraction_theta_max is the completeness (number measured/number reflections expected) at this angle.

Theta_full allows you to specify a value of theta at which you are prepared to call your data set 'complete'. Because 100% completeness is very tricky to acheive, there is no hard and fast rule for deciding where to set theta_full. By default, CRYSTALS will choose a value for you, trading off decreasing theta with increasing completeness (though it is worth noting that in many cases, a few missing reflections at low theta - e.g. due to beam stop - will mean that completeness actually increases with increasing theta). An analysis of completeness is given amongst the "Tabbed initial analysis" graphs from the "Analyse" menu in CRYSTALS.

If you just want a diagram, you can edit the cif by multiplying all the atomic coordinates by -1, but this isn't a good idea when producing material for publication.
It's generally better to do it in CRYSTALS:
For most space groups you can just use the 'invert structure' option from the 'structure' menu. Alternatively you can do the same thing from the command line by issuing:

 \edit
 transform -1 0 0 0 -1 0 0 0 -1 all
 end
 

These will probably give you a model in which the asymmetric unit lies well outside the standard unit cell. Look at a packing diagram in Cameron to find a better choice of molecule, save the changes then do another cycle of refinement. A new cif will have the correct symmetry operators if there are any bonds leading from one asymmetric unit to another, which is the main reason for not just modifying the original cif.
WARNING: there are certain space groups for which this procedure is insufficient. One type is where the space group contains a screw axis with a rotation component <180 degrees and all the symmetry operators have the same hand. In this case it is necessary to change the space group symbol. There are 11 pairs of this type: if your structure is one of these it should be interchanged with the other member of the pair:

 P 41      <-> P 43
 P 41 2 2  <-> P 43 2 2
 P 41 21 2 <-> P 43 21 2
 P 31      <-> P 32
 P 31 2 1  <-> P 32 2 1
 P 31 1 2  <-> P 32 1 2
 P 62      <-> P 64
 P 61      <-> P 65
 P 62 2 2  <-> P 64 2 2
 P 61 2 2  <-> P 65 2 2
 P 41 3 2  <-> P 43 3 2
 

Change the space group from the 'edit spacegroup' option of the 'X-ray data' menu, then invert the structure and choose the best asymmetric unit as above.
There are also 7 space groups in which the origin also has to be changed - the offending ones are:
F d d 2, I 41, I 41 2 2, I 41 m d, I 41 c d, I -4 2 d and F 41 3 2. If you have a structure in one of these, get help!


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