Received from John Helliwell and thus forwarded to the bb - why should
you miss important information?
-------- Original Message --------
Subject: Re: [ccp4bb] Accuracy of the position of coordinates
Date: Tue, 3 Aug 2010 09:08:30 +0100
From: John R Helliwell <[email protected]>
To: Vellieux Frederic <[email protected]>
References: <[email protected]>
Dear Fred,
I think the Cruickshank Diffraction Precision Index and its specific
reformulation by David Blow are a better estimate of overall coordinate
errors.
These two papers are in Acta D.
Greetings,
John
On Tue, Aug 3, 2010 at 8:41 AM, Vellieux Frederic
<[email protected] <mailto:[email protected]>> wrote:
> I would like to know the accuracy (error) of the position of the
coordinates
This is provided by the output of the refinement software.
An example (CNS-refined structure, from the pdb header, there is an
input file called "xtal_pdbsubmission.inp"
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36
REMARK 3 ESD FROM SIGMAA (A) : 0.45
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60
Another example, from Phenix:
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.41
A third example, from Refmac:
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A):
0.356
REMARK 3 ESU BASED ON FREE R VALUE (A):
0.279
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A):
0.282
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2):
12.096
Can't provide you with an example for Buster because I requested the
software last year and I do not know what happened to that request.
The coordinate errors are estimated using statistical methods.
Relevant papers to read are those of Randy Read and of Vittorio
Luzzatti (and probably of others), Luzzatti V. (1952), Acta Cryst.
5, 802-810; Read, R.J. (1986), Acta Cryst. A42, 140-149. There are
probably papers by "the Russian school" (Lunin and others) but I
can't locate them right now...
Fred.
--
Professor John R Helliwell DSc
