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: [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 >
