Tom, If this lady does indeed send you the data, Would you be so kind to run the latest version of xtriage on it to see wheter or not tyhe spacegroup is correct? Thomas C. Terwilliger wrote:

Hi Angela,

I think the solution to the first problem is to index your data in the space group H3 instead of R3 (the hexagonal setting of R3 rather than the rhombohedral setting). This is the convention these days in many programs, including in the AutoSol wizard.

The second problem I'm a little less clear on. Can you send me some output where this happens (or if you like, a tar file with the data) and I'll have a look at it? Regards, Tom T

...

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. Angela

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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 : http://cci.lbl.gov/cctbx/browse_settings.html 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() ) xs.show_summary() xs_new.show_summary() HTH Peter 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. Angela

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