You can also use phaser.famos to compare MR solutions to see if
they are related --
https://www.phaser.cimr.cam.ac.uk/index.php/Famos
phaser.famos moving.pdb=pdbfile1 fixed.pdb=pdbfile2
(from the it looks like there is also a phenix
GUI to access this functionality as well --
https://phenix-online.org/documentation/reference/find_alt_orig_sym_mate.html
)
Regards,
Mitch
(P.S. phenix.get_cc_mtz_mtz will also check for allowed origin
shifts to align maps output from 2 MR solutions).
https://phenix-online.org/documentation/reference/get_cc_mtz_mtz.html
Quoting Eleanor Dodson <[email protected]>:
You know there are alternative origins for P43212 - and a different MR
search very often will opt for a different origin..
from CCP4 doc
P4(123)2(1)2 - I4(1)22
N*origin*
Xo
Yo
Zo
1
0.0000
0.0000
0.0000
2
0.0000
0.0000
0.5000
3
0.5000
0.5000
0.0000
4
0.5000
0.5000
0.5000
Use
csymmmatch pdbin new-one.pdb pbin-ref old-one.pdb
Or
In CCP4I2 - task -Match model to original will suggest which change of
origin is needed.
On Mon, 6 Sept 2021 at 06:50, Ethan A Merritt <[email protected]> wrote:
Two questions
(1) What is the rotation+translation operation that relates
solution #1 an solution #2?
(2) Have you double-checked and then checked yet again that both
solutions are in P43212? Could it be that one of them ended
up in, say, P414241?
it's happened to me :-(
Ethan
On Sunday, 5 September 2021 21:45:39 PDT Lande Fu wrote:
> Dear all,
>
>
> Recently I had a strange problem related to MR and it confused me and my
colleagues a lot.
>
> My protein crystal was diffracted at 2.63A and I processed it normally
then did MR with Phaser (in P432(1)2). The result itself looked okay and
well fit the map. However, the R-work/ R-free value was stuck at
0.3012/0.2434 after cycles of manual refinement. Then I redid MR with
another model from PDB website and got another solution which looked
similar to previous one and the R-work/ R-free value can be lowered to
0.2496/0.1967 after refinement.
>
> Strange things appeared when I opened the two MR solutions in single
coot window (Fig 1). The two models were neither overlaying each other nor
on the symmetry of the other. The two models are nearly identical (actually
the first model was a previous structure built from PDB model) and have
same construct with my protein. There is no TNCS, twinning or other
noticeable problems detected according to aimless log.
>
> My question is: why phaser gives two different solutions from same map
and similar model and result in different R-work/ R-free value? Does that
mean there are two phases in the map? Does that imply multiple lattices in
my crystal?
>
> I tried to research myself but did not find any related explanation for
it. Please let me know if you need more information. Thank you in ahead.
>
>
> Regards,
>
> Lande Fu
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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