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Phil, Yes, but for some reason the intensities (or <F^2>) are frequently not present in mtz files. Maybe some other CCP4 program is removing them. 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, Phil Evans wrote: > 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 <[log in to unmask]> wrote: > > > > > > > > >From: Eleanor Dodson <[log in to unmask]> > > > > >Subject: Re: [ccp4bb] Lower completeness, decent R factors, > > > >but low B factor... > > > > >To: [log in to unmask] > > > > >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 > > >[log in to unmask] 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. 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