Hi Eleanor and Kay,
The unit-cells are nicely related. If we take the niggli cell of the I2
system and apply a (x-z,-y+z,-z) transformation, and subsequently multiply
the resulting z axis by 2, we get to the C2221 niggli cell with a fraction
of an Angstrom / Degree.
There are various C2 options as subgroups of C2221 - I don't know which one
we need here, the change of basis stuff makes it kinda opaque.
You can basically chain it together like
I2 -> I2_niggli -> I2_niggli_(x-z,-y+z,-z) -> double the c axis
the doubling of the c-axis essentially means that you turn a lattice
translation into a pseudo translation - I think.
xtriage indeed triages stuff - fixing comes later, if the dataset survives
that is.....
P
*METRIC SYMMETRY ANALYSIS*
phenix.explore_metric_symmetry --unit_cell="47.39, 80.131, 160.433, 90,
98.3786, 90" --space_group=I2 --other_unit_cell="47.458, 317.576, 80.126,
90, 90, 90" --other_space_group=C2221
A summary of the constructed point group graph object is given below
====================================================================
----------------------
Input crystal symmetry
----------------------
Unit cell: (47.39, 80.131, 160.433, 90.0, 98.3786, 90.0)
Unit cell volume: 602727.158897
Space group: I 1 2 1
--------------------------
Lattice symmetry deduction
--------------------------
Niggli cell: (47.39, 80.131, 89.70763658310626, 116.52722912425298,
97.69148423911008, 90.0)
Niggli cell volume: 301363.579448
Niggli transformed input symmetry: C 1 2 1 (-z,x+y,2*x)
Symmetry of Niggli cell: C 1 2 1 (-z,x+y,2*x)
All pointgroups that are both a subgroup of the lattice symmetry and
a supergroup of the Niggli transformed input symmetry wil now be listed,
as well as their minimal supergroups/maximal subgroups and symmetry
operators that generate them.
For each pointgroup, a list of compatible spacegroups will be listed.
Care is taken that there are no systematic absence violation with the
provided input spacegroup.
------------------------
Vertices and their edges
------------------------
Point group C 1 2 1 (-z,x+y,2*x) is a maximal subgroup of :
* None
-------------------------
Transforming point groups
-------------------------
----------------------
Compatible spacegroups
----------------------
Spacegroups compatible with a specified point group
**and** with the systematic absenses specified by the
input space group, are listed below.
Spacegroup candidates in point group C 1 2 1 (-z,x+y,2*x):
* C 1 2 1 160.53 80.13 47.39 90.00 81.40 90.00
A second unit cell has been specified.
A summary of the constructed point group graph object is given below
====================================================================
----------------------
Input crystal symmetry
----------------------
Unit cell: (47.458, 317.576, 80.126, 90.0, 90.0, 90.0)
Unit cell volume: 1207620.75639
Space group: C 2 2 21
--------------------------
Lattice symmetry deduction
--------------------------
Niggli cell: (47.458, 80.126, 160.55122044070544, 90.0, 98.49928506518853,
90.0)
Niggli cell volume: 603810.378194
Niggli transformed input symmetry: C 2 2 21 (-x+y,z,2*y)
Symmetry of Niggli cell: C 2 2 2 (x+y,z,2*x)
All pointgroups that are both a subgroup of the lattice symmetry and
a supergroup of the Niggli transformed input symmetry wil now be listed,
as well as their minimal supergroups/maximal subgroups and symmetry
operators that generate them.
For each pointgroup, a list of compatible spacegroups will be listed.
Care is taken that there are no systematic absence violation with the
provided input spacegroup.
------------------------
Vertices and their edges
------------------------
Point group C 2 2 2 (x+y,z,2*x) is a maximal subgroup of :
* None
-------------------------
Transforming point groups
-------------------------
----------------------
Compatible spacegroups
----------------------
Spacegroups compatible with a specified point group
**and** with the systematic absenses specified by the
input space group, are listed below.
Spacegroup candidates in point group C 2 2 2 (x+y,z,2*x):
* C 2 2 21 47.46 317.58 80.13 90.00 90.00 90.00
Unit cell comparison
--------------------
The unit cells will be compared. The smallest niggli cell,
will be used as a (semi-flexible) lego-block to see if it
can construct the larger Niggli cell.
Crystal symmetries in supplied setting
Target crystal symmetry:
Unit cell: (47.458, 317.576, 80.126, 90, 90, 90)
Space group: C 2 2 21 (No. 20)
Building block crystal symmetry:
Unit cell: (47.39, 80.131, 160.433, 90, 98.3786, 90)
Space group: I 1 2 1 (No. 5)
Crystal symmetries in Niggli setting
Target crystal symmetry:
Unit cell: (47.458, 80.126, 160.551, 90, 98.4993, 90)
Space group: C 2 2 21 (-x+y,z,2*y) (No. 20)
Building block (lego cell) crystal symmetry:
Unit cell: (47.39, 80.131, 89.7076, 116.527, 97.6915, 90)
Space group: C 1 2 1 (-z,x+y,2*x) (No. 5)
Volume ratio between target and lego cell: 2.00
Cartesian basis (column) vectors of lego cell:
/ 47.4 0.0 -12.0 \
| 0.0 80.1 -40.1 |
\ 0.0 0.0 79.4 /
Cartesian basis (column) vectors of target cell:
/ 47.5 0.0 -23.7 \
| 0.0 80.1 -0.0 |
\ 0.0 0.0 158.8 /
A total of 20 matrices in the hermite normal form have been generated.
The volume changes they cause lie between 3 and 2.
Trying all matrices
1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0
* . . . . . . . . | . . . . . . . . . |
Listing all possible solutions
Solution 1
--------------------------------------------------------------
Target unit cell : 47.5 80.1 160.6 90.0 98.5 90.0
Lego cell : 47.4 80.1 89.7 116.5 97.7 90.0
/ 1 0 0 \
matrix : M = | 0 1 0 |
\ 0 0 2 /
Additional Niggli transform: x-z,-y+z,-z
Additional similarity transform: x,y,z
Resulting unit cell : 47.4 80.1 160.4 90.0 98.4 90.0
Deviations : 0.1 -0.0 0.1 0.0 0.1 0.0
Deviations for unit cell lengths are listed in %.
Angular deviations are listed in degrees.
--------------------------------------------------------------
On Thu, Apr 17, 2025 at 12:49 PM Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:
> Dear Stefan,
>
> it strikes me that you say that the auto-processing (which software,
> synchrotron, beamline??) came up with I2. XDS itself would not suggest I2;
> it indexes in C2 (for reasons I try to explain in
> https://wiki.uni-konstanz.de/xds/index.php/Pointless). So there is likely
> some re-indexing going on, and that might be responsible for the
> discrepancy that Eleanor notes.
> Phenix.xtriage won't tell you about what the problem is; it just may show
> that there is a problem.
> I suggest you post IDXREF.LP (or send it to me privately).
>
> Best,
> Kay
>
> On Thu, 17 Apr 2025 03:13:59 +0100, Stefan Clarke <sclar...@fredhutch.org>
> wrote:
>
> >Dear CCP4 Community,
> >
> >I was hoping for some insight into a problem I am having with crystal
> data I collected.
> >
> >The data was auto-processed with XDS to 2.1Å with the I 1 2 1 space group
> . (Unit cell dimensions - 47.39, 80.131, 160.433, 90, 98.3786, 90.)
> >Running Xtriage in phenix showed the data likely contain translational
> pseudosymmetry however, Solvent and Matthews coefficient suggests there is
> only one copy of the protein complex in the asymmetric unit.
> >
> >
> >I managed to find a molecular replacement (MR) solution in phenix (using
> Phaser) for the protein complex and began refinements. The electron
> density map looks good and in agreement with a 2.1Å dataset. However, the
> refinement is stuck with high R-work and R-free values above 0.3 suggesting
> there may be an issue with the space group of the XDS auto-processed data
> or with the data.
> >
> >I re-processed the data using both HKL2000 and XDS. Both gave C 2 2 21 as
> the space group (Unit cell dimensions - 47.458, 317.576, 80.126, 90, 90,
> 90) and one copy of the complex is predicted to be in the asymmetric unit.
> However, I have not been able to find a MR solution with this new space
> group or its enantiomers using Phaser MR in phenix.
> >
> >Any suggestions and insight into this problem would be greatly
> appreciated. If anything needs to be clarified, I’ll try my best to do so.
> Thank you in advance.
> >
> >
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--
------------------------------------------------------------------------------------------
Peter Zwart
Staff Scientist, Molecular Biophysics and Integrated Bioimaging
Berkeley Synchrotron Infrared Structural Biology
Biosciences Lead, Center for Advanced Mathematics for Energy Research
Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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