Very easy in ccp4i2
Choose the task
reindex reflections or change spacegroup.
Select EXPAND
This will expand your data list to P1
Log file attached..
I did it for H3 to P1
Input 39694 reflections
Output 118919
It is possible your spacegroup really is P1 - I would reprocess the data in
P1 (or C1?) forcing it to keep the C2 cell and see if you will keep the C2
organisation of the big molecule but not the VHH
On Fri, 4 Sept 2026 at 14:06, Jon Cooper <
[email protected]> wrote:
> Hello, I don't really get what is going on here but are we thinking the
> antibody has partial occupancy?
>
> Best wishes, Jon Cooper (Emeritus at UCL) [email protected]
> Erratum and other hopefully useful things: https://crxp.org.uk
>
> Sent from Proton Mail for Android.
>
> -------- Original Message --------
> On Thursday, 09/03/26 at 21:39 Kay Diederichs <
> [email protected]> wrote:
> Hi Charlie,
>
> expanding to P1 can be done with CCP4 sftools (see
> https://www.ccp4.ac.uk/html/sftools.html#expand), or with
> phenix.reflection_file_converter --expand_to_p1 input.mtz --mtz=output.mtz
> (Maybe there's yet another CCP4 tool)
>
> Unfortunately, expanding removes the information about the differences of
> the molecules that are pseudo-symmetry related.
>
> I'd rather keep this information.
>
> Because scaling needs multipicity (which typically is poor in P1), I
> therefore suggest to scale in C2, but to merge in P1.
> 1. scaling in C2: If you use XDS, you obtain XDS_ASCII.HKL scaled in C2
> but since it is unmerged, its reflections retain the full P1 information.
> If you want to be more certain that large real differences between
> pseudo-symmetry related reflections are not considered as outliers in
> scaling, increase WFAC1 to (say) 2.
> 2. create XDSCONV.INP with SPACE_GROUP_NUMBER= 1, but the
> UNIT_CELL_PARAMETERS of the C2 cell
> 3. run XDSCONV to obtain a merged MTZ file in P1, with the C2 cell
> 4. run CCP4 reindex to obtain the conventional P1 cell
> (sorry that this is so cumbersome due to the reindexing)
>
> It is clear that the statistics you obtain from XDS in step 1 do not apply
> to the P1 data you obtain in step 3 and 4, but the data should be better
> than the expanded data. (And the expanded data have the same problem
> concerning their statistics)
>
> Hope this helps,
> Kay
>
> On Thu, 3 Sep 2026 11:22:35 +0000, Nichols, Charlie <
> [email protected]> wrote:
>
> >Hi,
> >
> >I have a very peculiar crystal structure which has been challenging to
> solve:
> >
> >Prot-X + VHH – nominally expected to be a 1:1 complex
> >
> >Data auto-process as C2
> >CRYST1 132.084 56.245 86.262 90.00 108.40 90.00 C 1 2 1
> >
> >2 copies of Prot-X easily located by molecular replacement, Phaser fails
> to find the VHH
> >
> >Manual assessment of density in crystal voids reveals a density patch
> about the right size / shape for a VHH.
> >Manual placement of a VHH into this density shows it lies across the C2
> 2-fold so the lattice symmetry places an inverted copy of the placed VHH in
> the same location.
> >
> >Expanding the symmetry to P1 gives 4-chains, arranged in a square ring,
> with a hole in the middle where the VHH sits, sterically only 1 VHH can sit
> in the hole
> >CRYST1 56.245 71.780 86.262 106.88 90.00 113.07 P 1
> >
> >I overlaid a computational model of Prot-X + VHH onto each of the 4
> chains, 2 positions align reasonably with the density (related by 2-fold as
> expected), the other 2 do not.
> >If I refine either of these models in P1 with twin refinement then I get
> a reasonable map, especially where the VHH contacts Prot-X as the
> alternative 2-fold related position does not overlap at the contact surface.
> >
> >Some parts of the density look really good, some are a bit confused /
> look like some rebuilding is required, though this may be largely residual
> density from the alternate orientation.
> >
> >Data resolution is modest with fairly noisy outer shell data so I can
> process to 2.6A with much better stats in C2 but only 2.8A and
> significantly worse stats in P1.
> >
> >I have had similar cases before in monoclinic/orthorhombic and
> trigonal/hexagonal and was able to obtain better maps by symmetry expanding
> the higher resolution processing from the higher symmetry spacegroup to the
> lower symmetry spacegroup rather than processing in the lower symmetry.
> >
> >I would therefore like to take the C2 processed data, symmetry expand to
> P1 and then use these expanded data for twin refinement to try and improve
> map quality.
> >
> >I am however not sure how to expand / transform the data from the C2
> lattice to the P1 case.
> >
> >Help appreciated…
> >
> >Thanks, Charlie.
> >
> >########################################################################
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
###############################################################
###############################################################
###############################################################
### CCP4 9.0.017: POINTLESS version 1.15.2 : 22/03/26##
###############################################################
User: eleanor Run date: 4/ 9/2026 Run time: 16:42:39
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67,
235-242.
as well as any specific reference in the program write-up.
==== Command line arguments ====
XMLOUT /Users/eleanor/CCP4I2_PROJECTS/TcECH/CCP4_JOBS/job_62/program.xml
HKLIN /Users/eleanor/CCP4I2_PROJECTS/TcECH/CCP4_JOBS/job_62/MergedToReindex.mtz
HKLOUT /Users/eleanor/CCP4I2_PROJECTS/TcECH/CCP4_JOBS/job_62/Reindexed.mtz
Release Date: 22nd March 2026
==== Input command lines ====
# Task 62 pointless_reindexToMatch running pointless
# Mini-MTZ input to HKLIN:
# Data type parameter job annotation
expand
end
==== End of input ====
******************************************************
* *
* POINTLESS *
* 1.15.2 *
* *
* Determine Laue group from unmerged intensities *
* Phil Evans MRC LMB, Cambridge *
* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
* *
******************************************************
HKL file
/Users/eleanor/CCP4I2_PROJECTS/TcECH/CCP4_JOBS/job_62/MergedToReindex.mtz
Spacegroup: H 3
Cell: 132.53 132.53 83.16 90.00 90.00 120.00
Columns for intensities I: Iplus, SIGIplus, Iminus, SIGIminus
Time for reading file(s): 0.072 secs
Highest resolution: 1.95
Unit cell: 132.53 132.53 83.16 90.00 90.00 120.00
Space group: H 3
===============================================================
Copying merged MTZ file from
/Users/eleanor/CCP4I2_PROJECTS/TcECH/CCP4_JOBS/job_62/MergedToReindex.mtz
to
/Users/eleanor/CCP4I2_PROJECTS/TcECH/CCP4_JOBS/job_62/Reindexed.mtz
Reindexing operator [h,k,l]
Real space tranformation of fractional coordinates:
Real space transformation (x,y,z)
(x') = ( 1 0 0 ) (x)
(y') ( 0 1 0 ) (y)
(z') ( 0 0 1 ) (z)
Determinant: 1.000
Data are expanded to space group P 1
Output space group: P 1
Unit Cells:
Crystal: HKL_base
Cell: 132.53 132.53 83.16 90.00 90.00 120.00
Crystal: xTcECHapoHAOOAP13021
Cell: 132.53 132.53 83.16 90.00 90.00 120.00
Anomalous pairs will be swapped if hand of indices hkl is changed in reducing
to asymmetric unit
Anomalous Column Label1 Label2 Type
I+, I- Iplus Iminus K
sigma(I+, I-) SIGIplus SIGIminus M
( 0, 1, -40)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -40)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -40)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -37)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -37)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -37)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -34)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -34)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -34)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -31)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -31)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -31)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -28)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -28)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -28)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -25)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -25)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -25)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -22)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
( 0, 1, -22)
Swapping columns Iplus Iminus
Swapping columns SIGIplus SIGIminus
... more swapped
118919 reflections copied to output file, sorted on h,k,l
39649 input reflections expanded to P1
Final point group choice has alternative indexing possibilities
Alternative indexing possibilities are marked '*' if the cells are
too different at the maximum resolution
CellDifference(A) ReindexOperator
1 0.0 [h,k,l]
2 0.0 [k,h,-l]
$TEXT:Reference: $$ Please cite $$
P.R.Evans, 'Scaling and assessment of data quality' Acta Cryst. D62, 72-82
(2006).
<a href="http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html";>
<b>PDF</b></a>
P.R.Evans, 'An introduction to data reduction: space-group determination,
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)
<a href="http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html";>
<b>PDF</b></a>
$$
JOB TITLE SECTION (PROCESSMANAGER)
Reindex reflections or change spacegroup
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
