Re: [ccp4bb] CSYMMATCH for help

[Eleanor Dodson]

As I am sure you know -
if you generate experimental phases from isomorphous or anomalous
scatterers the differences between the reflection pairs can be equally well
described by sites at (x,y,z) or (-x,-y,-z) .
In addition many spacegroups allow coordinates to be related to several
alternative origins. (eg orthorhombic SGS can have origin at (0,0,0)
(1/2,0,0) (1/2,1/2,0) etc etc - these are tabulated in the CCP4
documentation..)

These alternatives mean that a particular phase may be either  Phi or -PHI
or Phi + 180 or ...

CSYMMATCH checks whether two phase sets agree taking this into account
the "Hand "  test checks whether the phases are PHI or -PHI
The origin checks whether the phase sets are related to a different space
group origin.

Both tests are needed for experimental phasing.
For molecular replacement you should only need to check for alternative
origins..

OK?
Eleanor





On Fri, 18 Mar 2022 at 15:42, Paul Bond <
30b0cd59fccb-dmarc-requ...@jiscmail.ac.uk> wrote:

> The -origin-hand option is also useful for comparing molecular replacement
> solutions that may have different origins.
>
> I think the slides in Andrey Lebedev's presentation help to visualise this
> problem (specifically slides 49 & 50).
>
> https://www.ccp4.ac.uk/schools/DLS-2020/course_material/day03.01%20-%20Introduction%20to%20symmetry%20-%20Andrey%20Lebedev.pdf
>
> Cheers,
> Paul
>
>
> On Fri, 18 Mar 2022 at 15:20, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I don't know for sure, but I think the -origin-hand thing would be for
>> heavy atom work where both enantiomers of the solution can fit the data.
>> Cheers, Jon.C.
>>
>>
>> Sent from ProtonMail mobile
>>
>>
>>
>>  Original Message 
>> On 18 Mar 2022, 04:02, 付兴科_201928000807036 < fuxingke0...@163.com> wrote:
>>
>>
>> Dear Colleagues,
>>  In cysmmatch of CCP4, there is a keyworded input，“-origin-hand”. The
>> resolution with "-origin-hand" is very different from the resolution
>> without "-origin-hand". What's the mean of "origin shif" ? How does it
>> work?
>> The reference page is .
>>
>> I'm looking forward to your reply.
>>
>> Regards
>>
>>
>>
>> Best wishes,
>>
>> Fu Xingke
>> Institute of Physics CAS
>>
>>
>>
>>
>> --
>>
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>>
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>>
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>>
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Re: [ccp4bb] CSYMMATCH for help

[Paul Bond]

The -origin-hand option is also useful for comparing molecular replacement
solutions that may have different origins.

I think the slides in Andrey Lebedev's presentation help to visualise this
problem (specifically slides 49 & 50).
https://www.ccp4.ac.uk/schools/DLS-2020/course_material/day03.01%20-%20Introduction%20to%20symmetry%20-%20Andrey%20Lebedev.pdf

Cheers,
Paul


On Fri, 18 Mar 2022 at 15:20, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> I don't know for sure, but I think the -origin-hand thing would be for
> heavy atom work where both enantiomers of the solution can fit the data.
> Cheers, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 18 Mar 2022, 04:02, 付兴科_201928000807036 < fuxingke0...@163.com> wrote:
>
>
> Dear Colleagues,
>  In cysmmatch of CCP4, there is a keyworded input，“-origin-hand”. The
> resolution with "-origin-hand" is very different from the resolution
> without "-origin-hand". What's the mean of "origin shif" ? How does it
> work?
> The reference page is .
>
> I'm looking forward to your reply.
>
> Regards
>
>
>
> Best wishes,
>
> Fu Xingke
> Institute of Physics CAS
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] CSYMMATCH for help

[Jon Cooper]

I don't know for sure, but I think the -origin-hand thing would be for heavy 
atom work where both enantiomers of the solution can fit the data. Cheers, 
Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 18 Mar 2022, 04:02, 付兴科_201928000807036 wrote:

> Dear Colleagues,
>
> In cysmmatch of CCP4, there is a keyworded input，“-origin-hand”. The 
> resolution with "-origin-hand" is very different from the resolution without 
> "-origin-hand". What's the mean of "origin shif" ? How does it work?
> The reference page is .
>
> I'm looking forward to your reply.
>
> Regards
>
> Best wishes,
>
> Fu Xingke
>
> Institute of Physics CAS
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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[ccp4bb] CSYMMATCH for help-2

[付兴科_201928000807036]

Dear Colleagues,
 In cysmmatch of CCP4, there is a keyworded input，“-origin-hand”. The 
solution with "-origin-hand" is very different from the solution without 
"-origin-hand". What's the mean of "origin shif" ? How does it work?

The reference page is .
 

I'm looking forward to your reply.


Regards







Best wishes,

Fu Xingke

Institute of Physics CAS



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[ccp4bb] CSYMMATCH for help

[付兴科_201928000807036]

Dear Colleagues,
 In cysmmatch of CCP4, there is a keyworded input，“-origin-hand”. The 
resolution with "-origin-hand" is very different from the resolution without 
"-origin-hand". What's the mean of "origin shif" ? How does it work?

The reference page is .
 

I'm looking forward to your reply.


Regards







Best wishes,

Fu Xingke

Institute of Physics CAS



To unsubscribe from the CCP4BB list, click the following link:
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