Dear Ian, I agree entirely about the k-curve approach. SHELX/S/C/D/E have always used it to derive E-values.
Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 22 Aug 2008, Ian Tickle wrote: > > This indeed raises the question of whether the assumed Wilson > distribution is valid, and it's another point I was in fact going to > bring up. As presently constructed, Truncate fits a straight line to > the Wilson plot (based on Imeas) in order to determine the overall scale > & B, but to avoid the problem that the low res data for a typical > protein deviates markedly from the theoretical distribution, it uses > resolution limits determined by the RSCALE option. According to the man > page, the low resolution limit is by default set to 4 Ang if the high > res limit is higher than 3.5 Ang. This usually means that the straight > line fit is good for the high res data, but very poor for the low res > data, but at least this means that the assumed distribution is valid at > high res where most of the weak data (i.e. the data most affected by the > Bayes correction) is located, but not valid for any weak data at low res > (there will obviously be some). As you point out translational NCS > invalidates these assumptions since the form of the distribution > changes, but then probably only a few % of structures suffer from this > type of NCS. > > A better way to deal with this would surely be to forget about the > Wilson plot and simply determine the average I in resolution shells, > with perhaps spline interpolation between the bin means (this is > actually the 'k-curve' method for determining E's, attributed originally > to Karle & Hauptman I believe). There would still be an assumption of > the Wilson distribution but now only within the bins, i.e. the Wilson > distribution parameter would vary with resolution, when previously it > was a single number independent of resolution. I think this would go > some way towards addressing your objections. > > In fact my prog ECALC already uses the k-curve method to determine E's > and it would probably not be too much work to have it optionally read > the IMEAN column, perform the Bayes probability integrals and output > both <F> and <F^2> (also <E> & <E^2> as now). However I've no idea > whether my iteration idea for re-using the <F^2> values for the k-curve > will work - it may well diverge! > > Cheers > > -- Ian > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of George M. Sheldrick > > Sent: 22 August 2008 18:57 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Wilson plot from truncated.mtz > > > > In addition to Ian's circular argument, there is the problem that > > the assumed distribution is only approximately valid, indeed in the > > presence of (translational) NCS it could well be a poor approximation. > > Refinement against suitably weighted measured intensities > > (which may of > > course be slightly negative because of experimental errors) > > avoids this > > problem but we still need F(obs) (and hence TRUNCATE) to > > calculate a map. > > > > George > > > > Prof. George M. Sheldrick FRS > > Dept. Structural Chemistry, > > University of Goettingen, > > Tammannstr. 4, > > D37077 Goettingen, Germany > > Tel. +49-551-39-3021 or -3068 > > Fax. +49-551-39-22582 > > > > > > On Fri, 22 Aug 2008, Ian Tickle wrote: > > > > > This goes back to the issue I was raising, namely that > > <F>^2 (from the > > > Truncate output mtz F column) is not the same as Imeas (in the IMEAN > > > column) so you won't get exactly the same results from the > > Wilson plot, > > > particularly at high res where the average I/sigma is low. > > Since the > > > plot actually demands F^2 then it seems to me that > > logically you need to > > > use <F^2> which AFAICS is not possible using Truncate since it never > > > calculates that. > > > > > > This gets you into a circular argument because you need the correct > > > Wilson plot results in order to perform the Bayes correction to the > > > intensities (i.e. it gives you the prior distribution parameter), > > > however you need the Bayes-corrected intensities to > > correctly calculate > > > the Wilson plot! Possibly iterating (from the initial Wilson plot > > > results calculated using Imeas) will sort this out. > > > > > > Also referring to an earlier response by Phil, Truncate > > clearly outputs > > > the scaled Imeas, not <F^2>, in the IMEAN column as I had originally > > > assumed, since the column has a -ve min value from mtzdump > > (<F^2> can > > > never be < 0), and logically it's <F^2> not Imeas or <F> > > that you need > > > for applications (such as MR and F^2 based refinement) > > which demand F^2. > > > > > > Cheers > > > > > > -- Ian > > > > > > > -----Original Message----- > > > > From: [EMAIL PROTECTED] > > > > [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson > > > > Sent: 22 August 2008 14:16 > > > > To: [EMAIL PROTECTED] > > > > Cc: CCP4BB@jiscmail.ac.uk; [EMAIL PROTECTED] > > > > Subject: Re: Wilson plot from truncated.mtz > > > > > > > > rerun truncate with input amplitudes.. > > > > eleanor > > > > > > > > James Pauff wrote: > > > > > If I've lost my SCALA MTZ, and have only the truncated.mtz > > > > for my dataset, which program is the quickest means of > > > > obtaining a Wilson plot? > > > > > > > > > > Thank you again, > > > > > Jim > > > > > > > > > > > > > > > --- On Wed, 8/20/08, Eleanor Dodson > > <[EMAIL PROTECTED]> wrote: > > > > > > > > > > > > > > >> From: Eleanor Dodson <[EMAIL PROTECTED]> > > > > >> Subject: Re: [ccp4bb] Lower completeness, decent R > > > > factors, but low B factor... > > > > >> To: CCP4BB@JISCMAIL.AC.UK > > > > >> Date: Wednesday, August 20, 2008, 4:30 AM > > > > >> James Pauff wrote: > > > > >> > > > > >>> Hello all, > > > > >>> > > > > >>> I have a refined structure at 2.6 angstroms that at > > > > >>> > > > > >> about 73% completeness at this resolution. The I/sigma is > > > > >> about 2.0 at 2.6 angstroms, and the omit density for my > > > > >> ligands is great contoured at 3.0sigma. My Rcryst is 19 or > > > > >> so and the Rfree is 24.5 or so. > > > > >> > > > > >>> HOWEVER, my mean B value is 13.9, whereas my other 2 > > > > >>> > > > > >> structures (at 2.2 and 2.3 angstroms, same protein, >95% > > > > >> completeness) have mean B values of 22+. Any suggestions as > > > > >> to what is going on here? I'm having trouble explaining > > > > >> this. > > > > >> > > > > >>> Thank you, > > > > >>> Jim > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >> Have you used TLS - listed B factors will then be given > > > > >> relative to the > > > > >> TLS parameters. You need to run tLSANL to get a more > > > > >> realistic value. > > > > >> Eleanor > > > > >> > > > > >> > > > > >> But in fact temperature factors are rather harder to > > > > >> estimate at lower > > > > >> resolutions than higher. Look at your <Fo> and > > > > >> <Fc> curves v resolution > > > > >> ( part of a REFMAC loggraph) and you can see that sometimes > > > > >> the overall > > > > >> scaling struggles to get a reasonable fit.. > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Disclaimer > > > This communication is confidential and may contain > > privileged information intended solely for the named > > addressee(s). It may not be used or disclosed except for the > > purpose for which it has been sent. If you are not the > > intended recipient you must not review, use, disclose, copy, > > distribute or take any action in reliance upon it. 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