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: [email protected]; [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: [email protected] > > >> 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. If you have received this communication > in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] > and destroy all copies of the message and any attached documents. > Astex Therapeutics Ltd monitors, controls and protects all its messaging > traffic in compliance with its corporate email policy. The Company accepts no > liability or responsibility for any onward transmission or use of emails and > attachments having left the Astex Therapeutics domain. Unless expressly > stated, opinions in this message are those of the individual sender and not > of Astex Therapeutics Ltd. The recipient should check this email and any > attachments for the presence of computer viruses. Astex Therapeutics Ltd > accepts no liability for damage caused by any virus transmitted by this > email. E-mail is susceptible to data corruption, interception, unauthorized > amendment, and tampering, Astex Therapeutics Ltd only send and receive > e-mails on the basis that the Company is not liable for any such alteration > or any consequences thereof. > Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, > Cambridge CB4 0QA under number 3751674 >
