Absolute Structure

Frequently Asked Questions

Since we have developed the maximum likelihood/ Bayesian statistics approach of determining absolute structure we have received many questions about the practicalities of the method. This list attempts to answer these questions.

If any question remains, or any of the answers given here is unclear, please contact one of the authors for help.

How do I run the analysis using PLATON?

If you start PLATON, look in the REPORT column for the option BijvoetPair. You will need both a .cif and an .fcf file. If you execute this option, PLATON will perform several different analyses of the Bijvoet differences. The graph shown is a Delta-obs versus Delta-calc graph where the program fits a least squares line through the points. The distribution of the points in the cloud can be immediately indicative of the sign and reliability of the absolute structure assignment. Quantitative results are in the text column at the right. The values you will recognize for the y-analysis are the values under the header "Bayesian Statistics". Something that is not documented in the 2008 paper is that you have to pay attention to the Normal Probability Plot of which the parameters are listed just above the Bayesian values. It is important that the correlation coefficient is at least 0.999 showing that your errors are distributed as a Gaussian; if the correlation is lower than that you will have to take the results of the Bayesian analysis with a grain of salt (and most probably the Flack parameter as well....). For most good datasets we find that "Slope" is just under 1.0; if it is larger this is also a reason for concern as it tells you that the sigmas in your dataset are underestimated.

What is the Slope in PLATON? And the correlation coefficient?

The slope refers to the slope of a normal probability plot of Z-values for the Bijvoet pairs. This is calculated as a verification of the estimated standard uncertainties of the reflections. The slope should be around 1.0.

If the related correlation coefficient is smaller than 0.999, this may indicate a problem in the error model.

Since the maximum likelihood estimation of the absolute structure depends critically on the accuracy of the estimated standard uncertainties in the reflection intensities, it is critical that any deviations from 1.0 are researched before the values resulting from the calculation are used.

What do I do if the correlation coefficient in PLATON is smaller than 0.999?

You can click on the option "NPP-Bijvoet" in the command column. It shows the normal probability plot in ASCII graphics. Most likely you will find that the plot has a (slight) inverted "S" shape. This means that the error distribution is deviating from the normal distribution; outliers are more likely. In such cases the probability estimates given for P2 and P3 are too extreme, and the estimated standard uncertainty in y is too small. Our 2010 paper describes a method to deal with such cases automatically; this will be available in PLATON soon.

What does it mean if the Slope in PLATON is larger than 1.0?

If the slope is larger than 1.0, this indicates that the standard uncertainties in the reflection intensities may be underestimated. This should be checked. A future version of PLATON that implements our enhancements described in the 2010 paper will deal with this automatically.

What does it mean if the Slope in PLATON is smaller than 1.0?

We often observe that the slope is around 0.85-0.95. This can occur because the Bijvoet differences are determined more accurately than the two individual reflection intensities. Most probably, there are errors in the reflection intensity determination that affect both reflections of a pair in the same way (e.g. absorption).

Should I measure some sensitive reflections with extra care?

We have carefully avoided the need for this in our method. In fact, adding any data to the data set will always improve the result. It is a lot easier to add general redundancy to a data set than it is to go out and measure specific sensitve Friedel pairs using a CCD system. If you would go through the specific-pair effort, you would also get many other reflections measured on those frames, and adding those other reflections to the mix can only improve the result further.

How come the discrimination is so clear even though almost half of all Bijvoet differences are pointing the other way?

In every structure where determination of the absolute structure is difficult, for almost all Bijvoet pairs the difference is of the same order of magnitude as its standard uncertainty. In such a case one expects that almost half of all Bijvoet pairs is pointing in the wrong direction. Only by using the maximum likelihood approach the cumulative signal of all Bijvoet pairs can be picked up with full sensitivity. See also the brief description of the method

How sensitive is the determination of the absolute structure to inaccuracies in the model?

It is fairly insensitive to changes in the structure that only affect the non-anomalous scatterers. In early attempts we have tried to determine the absolute structure of a model refined without hydrogen atoms, and results were still surprisingly discriminative. Errors in the model that concern the anomalously scattering atoms will disrupt the correct absolute structure determination (most likely you will get the result that both absolute structures are equally (un)likely).

How reliable is this method to estimate the ratio of the two components in a racemic mixture?

There is very little experience with crystals that are inversion twins, and none with crystals for which the twin ratio had been determined using other means. Values are typically comparable to the Flack values. If you have interesting samples, we would like to hear from you. There is one check you can do yourself even if you are not able to share your data with us: Before trusting an off-zero value of y you should examine the PLATON output very carefully. It is essential that the normal probability plot has a good correlation coefficient and a slope around 1.0 (see also related questions above).

Do you have suggestions on how I can use the results in a publication?

I will assume that you did get satisfactory results. If you are sure that you are dealing with an enantiopure compound, the "ideal" way of reporting would be to mention P2(wrong). This value is not calculated explicitly by PLATON, but in most practical cases it is almost identical to P3(wrong).

To be exact P2(wrong) = P3(wrong) / [P3(right)+P3(wrong)].

The publication text could look like:

Analysis of the absolute structure using likelihood methods (Hooft, Straver & Spek, 2008) was performed using PLATON (Spek, 2010). The results indicated that the absolute structure had been correctly assigned. The method calculated that the probability that the structure is inverted is smaller than 1x10^-xyz.
These probability numbers are difficult to compare with numbers people know from the past. The "y" value, given as "Hooft" parameter in PLATON, is meant to satisfy this. It can be directly compared with the Flack x parameter. You could write:
The absolute structure parameter y (Hooft, Straver & Spek, 2008) was calculated using PLATON (Spek, 2010). The resulting value was y=0.qqq(sss) indicating that the absolute structure has probably been determined correctly.
You could add a sentence judging the standard uncertainty using the criteria set by Flack & Bernardinelli (2000).

Can I use this method in combination with SQUEEZE?

You will need to be extra careful when combining an absolute structure determination and SQUEEZE. The anomalous effect makes the scattering factors of atoms complex; they have a "real" and an "imaginary" component. The SQUEEZE procedure will only remove the real component of the solvent from the structure, the imaginary component will stay. Therefore, if the atoms with the strongest anomalous effect (the "heaviest") are in the squeezed solvent, you will not be able to determine the absolute structure reliably. If the anomalous effect of the squeezed solvent is negligible in compared to the anomalous effect in the main structure, the absolute structure determination can be combined with SQUEEZE without problems.

Why does PLATON give n/a for P2 and P3 values?

The P2 and P3 calculations assume that the structure is known to be a pure enantiomer or a 50/50 racemate or a pure enantiomer, respectively. If the calculations of y and G show that this assumption is likely false, PLATON will refuse to calculate P2 and P3 values. Most likely, therefore, if you get "n/a" you are dealing with an inversion twin with a ratio that differs from 1:1.

Can I determine the absolute structure if there is no oxygen atom?

Some people have achieved significant results even for structures containing no atoms heavier than carbon or nitrogen. This will only work if you are very careful, and use CuKa radiation. The anomalous diffraction coefficient for carbon at CuKa radiation is even larger than for oxygen at MoKa radiation. Both need the highest care during all phases of the structure determination: a very good crystal, a very clean mount, a high measurement multiplicity and very careful data reduction and refinement.

Is it not better to use a method that calculates the absolute structure during normal refinement?

No, apparently not. There have been suspicions that the absolute structure parameter can be significantly correlated with other structural parameters. If that would really be the case, a full matrix refinement that includes the absolute structure parameter would be much better. However, we have felt since our earliest experience with this method that this correlation does not show up when a complete data set, including Friedel pairs is used in a refinement. This has been confirmed by Simon Parsons et. al. in their 2013 paper (Acta Cryst. B69, 249-259), where they see no differences between our method (using Gaussian error distributions, the 2008 original) and their own full matrix refinements based on Friedel Quotients or Differences.