Re: [ccp4bb] SHELXD for help

[Kay Diederichs]

On Tue, 1 Mar 2022 18:06:34 +0800, fu  wrote:

>Dear Colleagues,
>I have two question.
>The first question is, in SHELXD, they use XPREP to calculate the 
> correlation coefficient(CCano) between the signed anomalous differences at 
> different wavelengths? What’s the meaning? And how to calculate it?  The 
> reference is 《Schneider, T.R. & Sheldrick, G.M. (2002). "Substructure 
> Solution with SHELXD", Acta Crystallogr. D58, 1772-1779》
> ...

Hello Fu,

SHELXD uses data that may come from XPREP or SHELXC (or other programs). SHELXC 
is available as part of CCP4 (like SHELXD) and has part of the functionality of 
XPREP; XPREP however is not free. SHELXC (or other programs) calculate CCano. 
Please see 
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=XPREP and 
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=SHELX_C/D/E .

Hope this helps,
Kay



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Re: [ccp4bb] SHELXD for help

[Jon Cooper]

The diagonal elements of the scale matrix are 1/a, 1/b and 1/c for orthogonal 
cells. It converts orthogonal coordinates to fractional. There should be more 
info on the rcsb.org website or in the ccp4 documentation e.g. for pdbset. 
Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 1 Mar 2022, 11:16, Dom Bellini - MRC LMB wrote:

> Hi Fu,
>
> "The SCALEn (n = 1, 2, or 3) records present the transformation from the 
> orthogonal coordinates as contained in the entry to fractional 
> crystallographic coordinates." (please see here 
> https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html)
>
> "The self-correlation coefficient for the anomalous signal should be above 
> 25% for a significant signal." (for example see here 
> https://www.ccp4.ac.uk/schools/Japan-2014/lectures/shelxcde_tutorial.pdf or
> here 
> (https://www.ccp4.ac.uk/schools/APS-2010/tutorials/shelx/tutorial_shelx_chicago2009.pdf).
>
> I hope this should help you or at least point you towards the right 
> directions.
>
> BW,
>
> D
>
> On 01/03/2022 10:06, fu wrote:
>
>> Dear Colleagues,
>>
>> I have two question.
>>
>> The first question is, in SHELXD, they use XPREP to calculate the 
>> correlation coefficient(CCano) between the signed anomalous differences at 
>> different wavelengths? What’s the meaning? And how to calculate it? The 
>> reference is 《Schneider, T.R. & Sheldrick, G.M. (2002). "Substructure 
>> Solution with SHELXD", Acta Crystallogr. D58, 1772-1779》
>>
>> Second, what is the "SCALE1 SCALE2 SCALE3" in following picture?
>>
>> Best wishes,
>>
>> Fu Xingke
>>
>> Institute of Physics CAS
>>
>> 从 Windows 版[邮件](https://go.microsoft.com/fwlink/?LinkId=550986)发送
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
> Dom Bellini, Xray Crystallography Facility (1S205)
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge Biomedical Campus
> Cambridge CB2 0QH
> Phone 01223 267839
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] SHELXD for help

[Dom Bellini - MRC LMB]

Hi Fu,

"The SCALEn (n = 1, 2, or 3) records present the transformation from the 
orthogonal coordinates as contained in the entry to fractional 
crystallographic coordinates." (please see here 
https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html)


"The self-correlation coefficient for the anomalous signal should be 
above 25% for a significant signal." (for example see here 
https://www.ccp4.ac.uk/schools/Japan-2014/lectures/shelxcde_tutorial.pdf or
here 
(https://www.ccp4.ac.uk/schools/APS-2010/tutorials/shelx/tutorial_shelx_chicago2009.pdf).


I hope this should help you or at least point you towards the right 
directions.


BW,

D












On 01/03/2022 10:06, fu wrote:



Dear Colleagues,


    I have two question.


    The first question is, in SHELXD, they use XPREP to calculate
the correlation coefficient(CCano) between the signed anomalous
differences at different wavelengths? What’s the meaning? And how
to calculate it?  The reference is 《Schneider, T.R. & Sheldrick,
G.M. (2002). "Substructure Solution with SHELXD", Acta
Crystallogr. D58, 1772-1779》


Second, what is the "SCALE1   SCALE2  SCALE3" in following picture?

Best wishes,

Fu Xingke

Institute of Physics CAS

从Windows 版邮件 发送




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--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839



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