You are right. After I sent the email to the bulletin board, I
realized that in R32 there must be more then unit cells but did not
send a correction.
Next time, I will check the space group before sending an email.
Best regards,
Herman
*Von:*Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
*Gesendet:* Donnerstag, 2. Juli 2015 15:48
*An:* Schreuder, Herman R&D/DE; CCP4BB@JISCMAIL.AC.UK
*Betreff:* RE: [ccp4bb] Rfree below Rwork
Hi Herman,
While you’re correct regarding increase in number of entities in the
asu upon lowering the symmetry, you’re not correct for specific case
of R32. One molecule per asu in R32 equals 18 molecules per asu in P1.
/Regards,/
//
/Vaheh Oganesyan/
/www.medimmune.com/
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
Of *herman.schreu...@sanofi.com <mailto:herman.schreu...@sanofi.com>
*Sent:* Wednesday, July 01, 2015 7:34 AM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] AW: [ccp4bb] Rfree below Rwork
Dear Boaz,
One can equally well describe a R32 crystal with one molecule in the
asymmetric unit as P1 and 6 molecules in the asymmetric unit. In this
case, the NCS in P1 is identical to the crystallographic symmetry in R32.
Best,
Herman
*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
von *Boaz Shaanan
*Gesendet:* Mittwoch, 1. Juli 2015 12:10
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* Re: [ccp4bb] Rfree below Rwork
Just wondering about Eleanor's interesting remark: would the Rf & Rw
go as low as reported by Wolfram (0.22) in case of a wrong space group?
Boaz
/Boaz Shaanan, Ph.D. //
/Dept. of Life Sciences /
/Ben-Gurion University of the Negev /
/Beer-Sheva 84105 /
/Israel /
//
/E-mail: bshaa...@bgu.ac.il <mailto:bshaa...@bgu.ac.il>/
/Phone: 972-8-647-2220 Skype: boaz.shaanan /
/Fax: 972-8-647-2992 or 972-8-646-1710 //
//
------------------------------------------------------------------------
*From:*CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Eleanor Dodson [eleanor.dod...@york.ac.uk]
*Sent:* Tuesday, June 30, 2015 8:55 PM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* Re: [ccp4bb] Rfree below Rwork
I suppose if I was the referee for this structure and your FreeR is so
close to the Rfactor I would ask you to ensure you had the right space
group - is the 6 fold NCS actually 2 fold NCS with a crystallographic
3 fold..
Cases occur where R32 is indexed as C2..
Certainly if the Rfree set is assigned randomly to reflections which
are symmetry equivalents then you see this phenomena of Rfree = Rfactor
Eleanor
On 30 June 2015 at 18:26, Gerard Bricogne <g...@globalphasing.com
<mailto:g...@globalphasing.com>> wrote:
Dear Wolfram,
I have a perhaps optimistic view of the effect of high-order NCS
on Rfree, in the sense that I don't view it as a "problem". People
have agonised to extreme degrees over the "difficulty" of choosing a
free set of reflections that would produce the expected gap between
Rwork and Rfree, and some of the conclusions were that you would need
to hide almost half of your data in some cases!
I think it is best to remember that the idea of cross-validation
by Rfree is to prevent overfitting, i.e. ending up with a model that
fits the amplitudes too well compared to how well it determines the
phases. In the case of high-order NCS (in your case, the U/V ratio
that the old papers on NCS identified as the key quantity to measure
the phasing power of NCS would be less than 0.1!) the phases and the
amplitudes are so tightly coupled that it is simply impossible to fit
the amplitudes without delivering phases of an equally good quality.
In other words there is no overfitting problem (provided you do have
good and complete data) and the difference between Rfree and Rwork is
simply within the bounds of the statistical spread of Rfree depending
on the free set chosen.
You are lucky to have 6-fold NCS, so don't let any reviewer
convince you that it is a curse, and make you suffer for it :-) .
With best wishes,
Gerard.
--
On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote:
> Hello,
> my question concerns refinement of a structure with 6-fold NCS (local
> automatic restraints in REFMAC) against 2.8 A data. The size of my
free set
> is 1172 selected in thin resolution shells (SFTOOLS) and
corresponding to
> 4.3 % of reflections.
> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have
0.227/0.224. Yes,
> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
> I understand that NCS stresses the independence assumption of the
free set.
> Am I correct in believing that Rfree *may* be smaller than Rcryst
even in
> the absence of a major mistake? My hope is that the combined wisdom of
> ccp4bb followers can point out my possible mistake, suggest tests
that I
> may perform to avoid them and, possibly, arguments in defense of a
> crystallographic model with Rfree < Rcryst.
> Many thanks,
> Wolfram Tempel
--
===============================================================
* *
* Gerard Bricogne g...@globalphasing.com
<mailto:g...@globalphasing.com> *
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<tel:%2B44-%280%291223-353033> *
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