lksbath
Hi all,
I'm using Topas with single crystal data and I would like to know if there are any ways to improve the fit on peak intensities? The red fit line usually under estimates the peak heights by about half. I have done the Durham Topas glycine tutorial and seen it is possible to get a really nice fit so wonder if it is a data issue or I'm missing certain refinement parameters?
Thanks,
Lucy
johnsoevans
Lucy,
With single crystal data there are far fewer things to think about than with powder data in topas. As you're just working with hkl values and F^2 everything to do with peak shape, peak positions, LP factors, etc has already been handled in your integration and data reduction software.
Calculated intensities (F^2's) will be primarily affected by your structural model and adps.
To get R-factors comparable to normal single crystal packages you might adjust "i_on_error_ratio_tolerance". Many single crystal packages will quote R-factors for I > 2 or 3 sigma only.
You might consider changing the default weighting scheme to mimic that in e.g. shelx.
You might have to consider an extinction correction if that's needed for your samples.
The other "trick" to get adps on H which mirror those in packages like crystals and shelx is to change to the 9 parameter description of scattering factors. Topas reads scattering factors from a file called "ATMSCAT.CPP" in the topas directory. If you click on "use_9f0.bat" or "use_11f0.bat" it will copy the corresponding file to this filename. When we tested with e.g. the glycine example a few years ago topas gave results essentially identical to those in crystals/shelx using the 9f0 set.
The final thing to remember is that the "pseudo powder pattern" plotted in the gui with lines joining intensities only has meaning at the points where lines meet. The blue experimental line could look very different to the red calculated line if just a few of the calculated or observed reflections are wrong. In some ways it's better not to plot the line and just plot the data points. Drawing each intensity as an impulse would be better still.
Hope that's some help.
John
lksbath
Hi John,
I added "i_on_error_ratio_tolerance 2" and this improved the fit. I have found the relevant page in the Technical Reference manual 4.1 for the two weighting schemes that can be applied to single crystal refinement. I'm not sure how to translate the shelx weighting scheme exactly to the Topas single crystal style but it looks like it is fairly similar to those in the manual. The shelx weighting scheme has an extra parameter of P:
weighting = 1 / [ σ^2 (Fo^2 ) + (aP)^2 + bP ]
where P is [ 2Fc^2 + Max(Fo^2 ,0) ]/3 and a and b are functions of the bragg angle/indices of reflection.
I read in the shelx manual that an extinction parameter (EXTI 0.001) should be refined when GOOF is high. I then saw in a paper by Simon Parsons (Acta B69, 2013, 249-259) that he applied an extinction correction to a single crystal data set in Topas as follows, in the str section:
prm ext 0.001
Is this the correct way to apply an extinction correction? I have been using Topas in the 9f0 format so that shouldn't be an issue here. Is it possible to plot just data points in Topas? Or is this done in excel etc.
I will add all these new things to my file and see where that gets me. Thanks John!
Lucy
johnsoevans
Lucy,
I guess Simon P has the extinction formula somewhere in his input file. You might contact him for that. It may be that he's also got the shelx weighting scheme in topas format. I think I did this years ago but don't have it to hand.
Draw data points only in the "display" button in the gui window for the individual dataset.
John
lksbath
Hi John,
I found the extinction formula in the input file (below) and have contacted him about it and also his weighting scheme.
prm ext 0.001 min 1e-6
scale_pks = ( 1 + 0.001* ext * (I_no_scale_pks/(Mobs Get(scale)))*Lam^3 / Sin(2 Th) )^(-.5);
Thanks for your help!
Lucy