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..
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