Hi Phil, My understanding is that the IMEAN/SIGIMEAN columns output by Truncate are simply copied over from the input columns as output by Scala (possibly scaled by the Wilson scale to make them absolute), or have I got this wrong? If so wouldn't it be better to rename the columns (e.g. IEXP, or FSQEXP) to avoid confusion? NB Imeas, <F>^2 and <F^2> are formally all different quantities: Imeas can be -ve but <F>^2 and <F^2> can't! There is still the issue that George pointed out that IMEAN (whether it's Imeas or <F^2>) is in any case often not usable and/or available for use in applications which demand F^2.
-- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans > Sent: 20 August 2008 20:25 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Wilson plot from truncated.mtz > > Truncate output does by default contain I (aka F^2) columns > Phil > > > On 20 Aug 2008, at 20:25, George M. Sheldrick wrote: > > > Ian, > > > > SHELXL users would also be very happy if mtz files routinely > > contained <F^2> and its esd, but I had long regarded this as a > > lost cause. > > > > 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 Wed, 20 Aug 2008, Ian Tickle wrote: > > > >> Hi Jim > >> > >> You can just run Truncate again, exactly as you did > before, but this > >> time using your truncated.mtz file as input, since it > contains the > >> same > >> IMEAN/SIGIMEAN columns output by Scala. It will also give you > >> another > >> output mtz file which should be identical to your input mtz (but I > >> haven't tested this!). Truncate will also allow you to assign the > >> F/SIGF columns to get a Wilson plot (but no output mtz), but note > >> that > >> this is formally incorrect since squaring <F> is not the same as > >> using > >> <F^2> (i.e. <F^2> = <F>^2 + var(F)). > >> > >> It seems to me that it would be better if in fact Truncate did > >> write out > >> a <F^2> column (as well as <F>), because this should > really be used > >> in > >> place of <F>^2 in Molecular Replacement, native Patterson, > F^2 based > >> refinement, or indeed anywhere where F^2 is demanded (note > that using > >> Imeas doesn't help because obviously it's not the same as <F^2> > >> either). > >> > >> Cheers > >> > >> -- Ian > >> > >>> 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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