Re: [ccp4bb] How to deal with tNCS?

[Jon Cooper]

Hello again, the R- and R-free are pretty high so there might be a problem with 
the space group or you may not have found all the molecules in the asymmetric 
unit. Are there big gaps in the packing with electron density to suggest 
additional molecules? Have you tried the option to input the current solution 
as a starting structure to see if the MR finds any more subunits. Is there any 
flexibility within your structure which could lead to domains having different 
orientations or visibility in your map? Can the model be split further into 
domains? The diffraction pattern does show a fair amount of splitting. MOSFLM 
might even be able to get additional lattices for you. I haven't done this 
stuff for a bit so others will know more about DIALS, etc ;-0 It would be good 
to see the results of twinning tests, if you have any. The one from CTRUNCATE, 
if you have it, is quite good.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 21 Jul 2023, 04:10, Lande wrote:

> Dear Eleanor and Jon,
>
> Thank you for your replies. My good datasets are in P212121 space group and 
> unit cell 56.67 60.53 67.51 90.00 90.00 90.00 ,2 copies in ASU. The tNCS one 
> is in C2221 space group and unit cell 122.32 134.88 55.45 90.00 90.00 90.00. 
> Matthews suggests 4 copies and I tried 4-6 copies to search in phaser (only 4 
> copies in solutions). For fractional coordinate, it is 1/2 and the 
> Rfree/Rwork is 0.4877/0.4466. This is another topic I can hardly found in 
> modern crystallography textbooks..
>
> Here I also attached the self rotaion fuction. I guess there might be 8 peaks 
> but honestly I have no idea how to read those graphs. There is another 
> screenshot of "more tNCS" image.
>
> Many thanks to your help.
>
> regards,
> Lande Fu
>
> ---
>
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Re: [ccp4bb] How to deal with tNCS?

[Eleanor Dodson]

No attachments Lande Fu?
Your C2221 cell is pretty obviously related to the orthorhombic one.
(a b c )-C2221 ~  (2b 2c a)P212121
The cell volume of C2221 cell is ~ 4 x P212121 cell. -
8 symmetry related copies for C2221 and 4 for P212121
so if there are 2 molecules in P212121 ASU you expect 4 in the C2221 ASU.

I would reindex your P212121 cell as k l h
then change coordinates to Y,X,X ( or probably easier just run MR
again against the reindexed data)

Then place those coordinates in the C2221 cell, do a bit of refinement, and
look for the next pair.
I dont understand this "iFor fractional coordinate, it is 1/2 "..

Can you run MOLREP for the C2221 data set and send the log - phaser logs
are far too verbose!
Eleanor

On Fri, 21 Jul 2023 at 14:45, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello again, the R- and R-free are pretty high so there might be a problem
> with the space group or you may not have found all the molecules in the
> asymmetric unit. Are there big gaps in the packing with electron density to
> suggest additional molecules? Have you tried the option to input the
> current solution as a starting structure to see if the MR finds any more
> subunits. Is there any flexibility within your structure which could lead
> to domains having different orientations or visibility in your map? Can the
> model be split further into domains? The diffraction pattern does show a
> fair amount of splitting. MOSFLM might even be able to get additional
> lattices for you. I haven't done this stuff for a bit so others will know
> more about DIALS, etc ;-0 It would be good to see the results of twinning
> tests, if you have any. The one from CTRUNCATE, if you have it, is quite
> good.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 21 Jul 2023, 04:10, Lande <
> 8bc2565720d4-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
>  Dear Eleanor and Jon,
>
> Thank you for your replies. My good datasets are in P212121 space group
> and unit cell 56.67 60.53 67.51 90.00 90.00 90.00 ,2 copies in ASU. The
> tNCS one is in C2221 space group and unit cell 122.32 134.88  55.45  90.00
> 90.00  90.00. Matthews suggests 4 copies and I tried 4-6 copies to search
> in phaser (only 4 copies in solutions).  For fractional coordinate, it is
> 1/2 and the Rfree/Rwork is 0.4877/0.4466. This is another topic I can
> hardly found in modern crystallography textbooks..
>
> Here I also attached the self rotaion fuction. I guess there might be 8
> peaks but honestly I have no idea how to read those graphs. There is
> another screenshot of "more tNCS" image.
>
> Many thanks to your help.
>
> regards,
> Lande Fu
>
>
> --
>
> 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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>
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>
>



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[Helen Ginn]

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Re: [ccp4bb] How to deal with tNCS?

[Diana Tomchick]

I would second what Eleanor has to say about the relationship of your C2221 
cell to the P212121 cell. When I have had cases where there is a peak in the 
self Patterson function that is as high as yours (99.471% is essentially 100%), 
it means that the peak at 1/2, 0, 0 in the self Patterson is equivalent in size 
to the origin peak of the self Patterson. This happened for me when I indexed 
the data with a unit cell that was twice the size of the correct cell. From 
what you present, it sounds as though you should try refining the model in the 
smaller, primitive cell.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)



On Jul 20, 2023, at 10:10 PM, Lande 
<8bc2565720d4-dmarc-requ...@jiscmail.ac.uk>
 wrote:


EXTERNAL MAIL


 Dear Eleanor and Jon,


Thank you for your replies. My good datasets are in P212121 space group and 
unit cell 56.67 60.53 67.51 90.00 90.00 90.00 ,2 copies in ASU. The tNCS one is 
in C2221 space group and unit cell 122.32 134.88  55.45  90.00  90.00  90.00. 
Matthews suggests 4 copies and I tried 4-6 copies to search in phaser (only 4 
copies in solutions).  For fractional coordinate, it is 1/2 and the Rfree/Rwork 
is 0.4877/0.4466. This is another topic I can hardly found in modern 
crystallography textbooks..



Here I also attached the self rotaion fuction. I guess there might be 8 peaks 
but honestly I have no idea how to read those graphs. There is another 
screenshot of "more tNCS" image.


Many thanks to your help.


regards,
Lande Fu







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