JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCP4BB Archives


CCP4BB Archives

CCP4BB Archives


CCP4BB@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCP4BB Home

CCP4BB Home

CCP4BB  November 2013

CCP4BB November 2013

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

From:

Tim Gruene <[log in to unmask]>

Reply-To:

Tim Gruene <[log in to unmask]>

Date:

Thu, 7 Nov 2013 09:56:23 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (163 lines)

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Dear Jens,

thanks for setting this right.

Best,
Tim

On 11/07/2013 07:53 AM, Jens Kaiser wrote:
> Fulvio, Tim, error propagation is correct, but wrongly applied in
> Tim's example. s_f= \sqrt{ \left(\frac{\partial f}{\partial {x}
> }\right)^2 s_x^2 + \left(\frac{\partial f}{\partial {y} }\right)^2
> s_y^2 + \left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 +
> ...} (see 
> http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
>
> 
The uncertainty in a derived magnitude is always larger than any
> individual uncertainty, so no subtraction, anytime. Furthermore,
> in Tim's example you could end up with negative sigmas..
> 
> HTH,
> 
> Jens
> 
> 
> On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
> 
>> Dear Fulvio,
>> 
>> with simple error propagation, the error would be sigma(I(h1)) =
>> (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
>> 
>> would it not?
>> 
>> Although especially for theoretical aspects you should be
>> concerned about division by zero.
>> 
>> Best, Tim
>> 
>> On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
>>> Thank you for reply. My question mostly concern a theoretical 
>>> aspect rather than practical one. To be not misunderstood, what
>>> is the mathematical model that one should apply to be able to
>>> deal with twinned intensities with their errors? I mean,
>>> I+_what? I ask this In order to state some general
>>> consideration on the accuracy about the recovery the true
>>> intensities on varying of alpha. Thanks Fulvio
>>> 
>>> Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza 
>>> University of Rome 5, Piazzale A. Moro 00185 phone +39
>>> 0649910556
>>> 
>>> ----Messaggio Originale---- Da: [log in to unmask] 
>>> Inviato:  06/11/2013, 17:25 A: [log in to unmask] Oggetto: 
>>> [ccp4bb] AW: [ccp4bb] uncertainites associated with
>>> intensities from twinned crystals
>>> 
>>> 
>>> Dear Fulvio, you cannot detwin perfectly twinned data with
>>> this formula. The term (1-2α) becomes zero, so you are dividing
>>> by zero. With good refinement programs (ShelX, Refmac),
>>> refinement is done against twinned data, which is better than
>>> to detwin the data with the formula you mention.
>>> 
>>> As I understand it, to get map coefficients, the calculated 
>>> contribution of the twin domain (Fcalc’s) is substracted from
>>> Fobs (with the appropriate weighting factors), so what you see
>>> in coot is detwinned electron density. In practical terms, the
>>> only thing you have to do is to specify the TWIN keyword in
>>> Refmac.
>>> 
>>> Best regards, Herman
>>> 
>>> 
>>> 
>>> Von: CCP4 bulletin board [mailto:[log in to unmask]] Im
>>> Auftrag von Fulvio Saccoccia Gesendet: Mittwoch, 6. November
>>> 2013 16:58 An: [log in to unmask] Betreff: [ccp4bb]
>>> uncertainites associated with intensities from twinned
>>> crystals
>>> 
>>> 
>>> Dear ccp4 users
>>> 
>>> a question about the recovering of true intensities from
>>> merohedral twinned crystal. Providing alpha and the twin
>>> operator one should be able to recover the intensities from the
>>> formulas:
>>> 
>>> 
>>> 
>>> I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
>>> 
>>> I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
>>> 
>>> as stated in many papers and books*.
>>> 
>>> However I was wondering about the uncertainties associated to
>>> these measurements, I mean: for all physical observable an
>>> uncertainty should be given.
>>> 
>>> Hence, what is the uncertainty associated to a perfect
>>> merohedrally twinned crystal (alpha=0.5)? It is clear that in
>>> this case we drop in a singular value of the above formulas.
>>> 
>>> Please, let me know your hints or your concerns on the matter. 
>>> Probably there is something that it is not so clear to me.
>>> 
>>> 
>>> 
>>> Thanks in advance
>>> 
>>> 
>>> 
>>> Fulvio
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo,
>>> M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M.
>>> Catti. Fundamentals of Crystallography, 3rd edition. IUCr Texts
>>> on Crystallography No. 15, IUCr/Oxford University Press, 2011; 
>>> Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst.
>>> D55. 1750-1758)
>>> 
>>> --
>>> 
>>> Fulvio Saccoccia, PhD
>>> 
>>> Dept. of Biochemical Sciences "A. Rossi Fanelli"
>>> 
>>> Sapienza University of Rome
>>> 
>>> Tel. +39 0649910556
>>> 
>> 
> 
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFSe1W3UxlJ7aRr7hoRAtccAJ9vricfip29REbi54KT4ltpQBpCuwCggfoQ
HG6ZnqlPZ7uATrS6fTLDeyk=
=Shmh
-----END PGP SIGNATURE-----

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager