"ESDs and estimated probable-error obtained in rietveld refinements with local correlations" J.F. Berar and P. Lelann, Journal of Applied Crystallography, 1991, Vol.24, No.Pt1, pp.1-5.
McCusker, L. B., Von Dreele, R. B., Cox, D. E., Louër, D. & Scardi, P. (1999). J. Appl. Cryst. 32, 36-50.
Hugo Rietveld - Rietveld Method Web-site
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To: sdpd@egroups.com From: Steve Maginn [maginn@ccdc.cam.ac.uk] Date: Tue, 23 Jan 2001 10:41:11 +0000 Reply-To: sdpd@egroups.com Subject: [sdpd] error measurements Hi everyone, With an increasing number of structures being determined ab initio from powder data, the Cambridge Crystallographic Data Centre is beginning to grapple with the problems of inclusion of these into the Cambridge Structural Database. There is no doubt that they should or will be included, but one problem is that there appears to be little consistency or standard about which error measurement is used to give a quality indicator for structures. There are a plethora of different R-factors, chi squareds, etc. And the problem of course is relating these to the standard R and weighted R used in single-crystal structure determinations, with which powder structures will be compared when they join the bulk of crystallographic data in the CSD. Are there any views as to which error measurement should be used ? And how long will it be before reported powder structures are standardised using this measurement, so database authors and more importantly users can reliably judge the precision / quality of a structure ? Views welcome ... Cheers, Steve Maginn, CCDC, UK ===================================================== Dr. Stephen J. Maginn, Support and Marketing Manager, Cambridge Crystallographic Data Centre (CCDC), 12 Union Road, Cambridge CB2 1EZ, UK phone +44 (0)1223 762534 FAX +44 (0)1223 331116 e-mail maginn@ccdc.cam.ac.uk http://www.ccdc.cam.ac.uk ===================================================== |
To: sdpd@egroups.com From: Armel Le Bail [armel@fluo.univ-lemans.fr] Date: Tue, 23 Jan 2001 14:45:40 +0100 Subject: Re: [sdpd] error measurements >Are there any views as to which error measurement should be used ? And how >long will it be before reported powder structures are standardised using >this measurement, so database authors and more importantly users can >reliably judge the precision / quality of a structure ? That question is an endless controversy. However, see §11, page 47 in McCusker, L. B., Von Dreele, R. B., Cox, D. E., Louër, D. & Scardi, P. (1999). J. Appl. Cryst. 32, 36-50. The problem is that if you follow the recommendations, you will have to give not only some R values, but also a plot of the observed and calculated data with a scale magnification at large angle for X-ray data ;-). About R values, I prefer the conventional Rp and Rwp values (background subtracted, peak only contributions) plus the Rexp and the RB and RF values. The X**2 (goodness of fit) can be calculated from the Rwp/Rexp ratio. But you should not accept only X**2 without the Rwp and Rexp values, IMHO. A problem can be that people give Rp and Rwp without background subtraction, and without even saying it. And what about structures refined with many restraints and/or constraints and with the (number of reflections)/(number of refined parameters) quite small (< 3 or even < 1) ? They can give very good R values while being somewhat dubious. At least, they are more dubious than structures refined with such a ratio > 10. Thus, giving that ratio is an important information too. Hope this help. Armel Le Bail http://sdpd.univ-lemans.fr/course/ |
From: "Peter Y. Zavalij" [zavalij@binghamton.edu] Date: Tue, 23 Jan 2001 09:40:31 -0500 Subject: RE: [sdpd] error measurements I think the main 2 R-factors should be Rp and R(bragg) or R(F2) of course with background subtracted. >From my point these 2 values characterize Rietveld refinement similarly to Rw and RF in single crystal refinement. The other R-factors especially Rwp and Rexp should be taking into account as additional merits as well. On the other hand Armel is right simple look on the difference plot and other refinement parameters and restrictions can tell a lot about the structure quality too. It seems that some work on powder CIF is going on right now and it would be also useful what are IUCr requirements for submission of the powder refinement in Acta Cryst. Dr. Peter Y. Zavalij University Crystallographer Materials Research Center, SUNY at Binghamton Tel: (607)777-4298 Fax: (607)777-4623 E-mail:zavalij@binghamton.edu http://materials.binghamton.edu/zavalij |
From: cockcroft@gordon.cryst.bbk.ac.uk
Date: Tue, 23 Jan 2001 14:36:02 GMT
Reply-To: sdpd@egroups.com
Subject: Re: [sdpd] error measurements
I agree 100% with Armel about R-factors (and illustrate in particular
about the effect on background subtraction in our PD web course at
Birkbeck). I suspect the output of some programs are not very clear
concerning R-factors (or even weights - since I suspect there are still
many that use unit weights (i.e. non at all!)). I pointed out some
of these problems recently at CDCC, but as I said during my talk,
there will always be those who like to quote R-factors including
background because the numbers are lower, and there will always be
those who quote chi-squared values only becuase they wish to hide the
fact that the data is not of the highest quality.
Just the opinion of another powder crystalllographer,
Jeremy Karl cockcroft.
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From: cockcroft@gordon.cryst.bbk.ac.uk Date: Tue, 23 Jan 2001 14:54:40 GMT Reply-To: sdpd@egroups.com Subject: Re: [sdpd] error measurements To add to my recent comments, I disagree with quoting Rp (as used in the original JAC paper) - weights should be used - especially when X-ray data is collected repeatedly at higher two-theta angles so as to improve statistics. So I disagree with you, Peter Zavalij, re the use of Rp. I would also add that R-factors based on both total peak intensities and structure factors-squared are also useful, but they should be treated with some caution if the data has been collected for different time periods for different two-theta ranges (since they are difficult to weight properly). Jeremy Karl Cockcroft School of Crystallography, Birkbeck College, UK. |
To: sdpd@egroups.com From: Jaap Vente [jaap@jade.mda.cinvestav.mx] Date: Tue, 23 Jan 2001 10:02:28 -0600 (CST) Reply-To: sdpd@egroups.com Subject: Re: [sdpd] error measurements The pain with background substraction CAN be that you have high values with a further 'perfect' fit. In my experience this has often to do the presence of a relative large amount of peaks with low intensity. You may argue that you should measure longer under these circumstances, or reduce the 2 theta angle you are using. Even so, the improvement is minor if you have a low symmetry structure with atoms having very different scattering factors (heavy metal oxides for instance). And yes your Rwp might than be more an indication of how good the back ground has been fitted. High background level gives a nice and low Rwp. With this in mind I think that at the moment of writing there is no proper figure of merit for a Rietveld refinement, and yes the diffraction pattern should be available. I am sure that Steve Maginn is happy with this view :-). By the way I assume that the background is never substracted in the Rwp unless stated otherwise. Best wishes Jaap Jaap Vente Cinvestav-IPN Unidad Merida Departamento de Fisica Aplicada Carretera Ant. a Progreso km 6 Apartado Postal #73 Cordemex Merida, Yucatan, 97310 Mexico Fax: +52 (9) 981 29 17 Tel: +52 (9) 981 29 60 ext 243/230 e-mail: jaap@mda.cinvestav.mx web: http://www.mda.cinvestav.mx/ |
To: sdpd@egroups.com From: Steve Maginn [maginn@ccdc.cam.ac.uk] Date: Tue, 23 Jan 2001 16:17:23 +0000 Reply-To: sdpd@egroups.com Subject: Re: [sdpd] error measurements This - and indeed those that have come before - is a very interesting point of view. The storing of the whole diffraction pattern with a crystal structure is of course impossible with the current file formats of the Cambridge Structural Database, so I'm very happy with the view, but not happy to have to say that at the moment it is impossible to realise it ! That's not to say that it won't be possible at some time in the future ... This is all very valuable and helpful information for us - please keep it coming. Cheers, Steve Maginn |
To: sdpd@egroups.com From: cockcroft@gordon.cryst.bbk.ac.uk Date: Tue, 23 Jan 2001 16:22:26 GMT Reply-To: sdpd@egroups.com Subject: Re: [sdpd] error measurements I think one point re background subtraction in Rwp is being missed. Background count can be subtracted before the refinement process (as in the original Rietveld) or after using the refinable background function, i.e. the calculated background is subtracted. Both can easily be done. Also, in the summation process, profile point should not be included where there is no diffraction information. Jeremy Karl Cockcroft. |
To: sdpd@egroups.com From: Jaap Vente [jaap@jade.mda.cinvestav.mx] Date: Tue, 23 Jan 2001 12:15:22 -0600 (CST) Reply-To: sdpd@egroups.com Subject: Re: [sdpd] error measurements I agree with Jeremy Cockcroft that in THEORY you can substract the background both before and after refinement. The first option is actually rather difficult when you have peaks close to each other or with overlapping peaks. Or you must assume a constant background or so. The second option cause problems due to correlations between thermal and/or displacement parameters and the background. I think we all would agree very quickly on how to treat SrO and get reliable values, but life is not so easy with the more complicated structures. Jaap Vente Cinvestav-IPN Unidad Merida Departamento de Fisica Aplicada Carretera Ant. a Progreso km 6 Apartado Postal #73 Cordemex Merida, Yucatan, 97310 Mexico Fax: +52 (9) 981 29 17 Tel: +52 (9) 981 29 60 ext 243/230 e-mail: jaap@mda.cinvestav.mx web: http://www.mda.cinvestav.mx/ |