[phenixbb] unknown space group problems

Peter Zwart PHZwart at lbl.gov
Wed Mar 1 14:33:16 PST 2006

Dear Eric,

For sg  R3, you have two main settings:
R3:H : a=b!=c, 90,90, 120
R3:R: a=b=c, alpha=beta=gamma!=90
They are related of course.

please check :


and type

R3 in the space group box.

This will give two space group info charts that you can have a look at.

In this case (159.0, 159.0, 159.0, 109.0, 109.0, 109.0; R3:R) you 
actually will get
R 3:H  258.89 258.89 162.66 90.00 90.00 120.00
after transforming to the reference setting.

Note that higher metric symmetry is possible as well in this case, 
suggesting cubic symmetry:

Input crystal symmetry
Unit cell:  (159.0, 159.0, 159.0, 109.0, 109.0, 109.0)
Unit cell volume:  3147178.10148
Space group:  R 3 :R

( ...... )

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 R 3 2 :R:
  * R 3 2 :H  258.89 258.89 162.66 90.00 90.00 120.00

Spacegroup candidates in point group Hall:  I 2 2 3 (y+z,x+z,x+y):
  * I 2 3  184.66 184.66 184.66 90.00 90.00 90.00
  * I 21 3  184.66 184.66 184.66 90.00 90.00 90.00

Spacegroup candidates in point group R 3 :R:
  * R 3 :H  258.89 258.89 162.66 90.00 90.00 120.00

Spacegroup candidates in point group Hall:  I 4 2 3 (y+z,x+z,x+y):
  * I 4 3 2  184.66 184.66 184.66 90.00 90.00 90.00
  * I 41 3 2  184.66 184.66 184.66 90.00 90.00 90.00

(This list was generated with the following command:

iotbx.ehms --unit_cell='159 159 159 109 109 109' --space_group=R3:R.

In the absense of perfect twinning, xtriage should be able to figure out 
what the proper space group is)

Making something in the cctbx, something like this (not tested) should 
work I think:

from cctbx import uctbx
from cctbx import crystal
xs = crystal.symmetry( uctbx.unit_cell('30,30,30,109,109,109',
                                   'R3:R' )
xs_new = xs.change_basis( 
xs.space_group_info().change_of_basis_op_to_reference_setting() )



Erik Mckee wrote:

>Perhaps I am a bit confused here, but doesn't R3 require alpha=beta=90 and
>gamma=120?  Or, is this what is meant by the hexagonal setting?
>On Wed, 1 Mar 2006, Angela Hoffort wrote:
>>I am trying to sovle MAD data using the PHENIX software. I am using the AutoSol
>>wizard. My data is integrated in R3. Phenix keeps spitting out the error that
>>this space group is either unknown or the cell dimensions are inappropriate to
>>the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a glitch
>>with thi space group or am I doing something wrong. Phaser tends to have the
>>same problem with this space group and I can not seem to get around it.
>>If I provide data in a different space group I can get past this problem only to
>>be confronted with another problem regarding the column labels in my mtz files.
>>I have six data sets collected. Two for each of three different wavelengths.
>>Each of the two for a single wavelength is scaled seperately and then merged
>>together using ccp4. I have taken a lot of effort to make sure that the column
>>labels do not repeat in these files, yet I continually get column label errors
>>when I run three mtz files in the AutoSol wizard (one mtz file for each
>>wavelength). I am getting the same errors in ccp4 as well. There must be
>>something basic that I am doing wrong with regards to processing my data and
>>merging the mtzs together.
>>Thanks you for your help.
>>phenixbb mailing list
>>phenixbb at phenix-online.org
>phenixbb mailing list
>phenixbb at phenix-online.org
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