Re: [ccp4bb] Wilson plot from truncated.mtz

Sat, 23 Aug 2008 00:09:58 -0700

Actually Truncate (& ctruncate) do use a smoothed <I> in resolution shell (using a spline fit), not a linear Wilson plot 

Phil



On 22 Aug 2008, at 20:30, Ian Tickle wrote:


This indeed raises the question of whether the assumed Wilson
distribution is valid, and it's another point I was in fact going to
bring up.  As presently constructed, Truncate fits a straight line to
the Wilson plot (based on Imeas) in order to determine the overall scale 
& B, but to avoid the problem that the low res data for a typical
protein deviates markedly from the theoretical distribution, it uses
resolution limits determined by the RSCALE option. According to the man 
page, the low resolution limit is by default set to 4 Ang if the high
res limit is higher than 3.5 Ang. This usually means that the straight 
line fit is good for the high res data, but very poor for the low res
data, but at least this means that the assumed distribution is valid at high res where most of the weak data (i.e. the data most affected by the Bayes correction) is located, but not valid for any weak data at low res 
(there will obviously be some).  As you point out translational NCS
invalidates these assumptions since the form of the distribution
changes, but then probably only a few % of structures suffer from this
type of NCS.

A better way to deal with this would surely be to forget about the
Wilson plot and simply determine the average I in resolution shells,
with perhaps spline interpolation between the bin means (this is
actually the 'k-curve' method for determining E's, attributed originally 
to Karle & Hauptman I believe).  There would still be an assumption of
the Wilson distribution but now only within the bins, i.e. the Wilson
distribution parameter would vary with resolution, when previously it
was a single number independent of resolution.  I think this would go
some way towards addressing your objections.

In fact my prog ECALC already uses the k-curve method to determine E's
and it would probably not be too much work to have it optionally read
the IMEAN column, perform the Bayes probability integrals and output
both <F> and <F^2> (also <E> & <E^2> as now).  However I've no idea
whether my iteration idea for re-using the <F^2> values for the k- curve 
will work - it may well diverge!

Cheers

-- Ian


-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of George M. Sheldrick
Sent: 22 August 2008 18:57
To: [email protected]
Subject: Re: [ccp4bb] Wilson plot from truncated.mtz

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








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

Reply via email to