Re: [ccp4bb] process data in R32
As far as I know all the programs we use will handle the non-primitive hexagonal setting of rhombohedral space groups (ie a=b != c, alpha=beta=90, gamma =120), often denoted H3 or H32 (aka R3:H in cctbx). Many of them will probably handle the primitive rhombohedral setting (a=b=c, alpha=beta=gamma), but this is much less commonly used in macromolecular crystallography, so some programs may fail to do the right thing (though they should). A space group denoted R3 or R32 may be in either setting, depending on the cell dimensions. I don't know what HKL2000 does, but H32 is not primitive, it is the centred hexagonal setting. The paper cited by Ivan presumably used the hexagonal setting, since they had c != a or b confusing I know Phil On 12 Aug 2010, at 00:42, xaravich ivan wrote: Hello Ray, You can contact the author of this paper. It seems they used denzo scalpack for R32. Ivan On Wed, Aug 11, 2010 at 8:53 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: If you cant import a file with symmetry labelled R32 but with a=b and alpha=beta = 90, and gamma = 120 then something is wrong - the symmetry checking looks at both name and cell.. or at least it used to.. The output mtz would have symmetry name changed to H32, but that is just a name - in each case the sym ops and cell should be h32 style.. Eleanor Ray Brown wrote: Hi, I have read all of the past messages about the confusion of H32 and R32 and I want to get the correct indexing sp that I can import the .sca file into CCP4.. I use DENZO and SCALEPACK in HKL2000. If you read the manual then it states that space group R32 should only be autoindexed by DENZO on a primitive lattice using the DENZO keyword H32. This indeed gives a primitive unit cell and not the hexagonal setting apparently demanded by CCP4 programs. What do you do next? It is possible in SCALEPACK to reindex the H32 primitive data into a rhombohedral hexagonal setting which SCALEPACK calls R32. Or course you cannot import this .sca file into CCP4. Why not? I can go into the .sca file and edit the header and change the R32 label to H32. Does this screw up the indexing? If anybody has successfully used DENZO/SCALEPACK/CCP4 in space group R32 then please tell me how to do it correctly. Cheers. Ray email ray-br...@att.net am0110-1.pdf
Re: [ccp4bb] process data in R32
Coming from small molecule crystallography where this problem simply doesn't exit, I found it very difficult to understand all the fuss! The small molecule crystallographers specify the symmetry operations rather than the space group so there is nothing special about using different settings. If a program insists on starting from the space group name or number, a simple solution is to treat 'R32' and 'H32' as synonymous and to check the unit-cell dimensions to see which of the two settings it is. This requires one extra line of computer code and eliminates the problem. I know that many programs do it this way already, but unfortunately there are still a few black sheep. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Thu, 12 Aug 2010, Phil Evans wrote: As far as I know all the programs we use will handle the non-primitive hexagonal setting of rhombohedral space groups (ie a=b != c, alpha=beta=90, gamma =120), often denoted H3 or H32 (aka R3:H in cctbx). Many of them will probably handle the primitive rhombohedral setting (a=b=c, alpha=beta=gamma), but this is much less commonly used in macromolecular crystallography, so some programs may fail to do the right thing (though they should). A space group denoted R3 or R32 may be in either setting, depending on the cell dimensions. I don't know what HKL2000 does, but H32 is not primitive, it is the centred hexagonal setting. The paper cited by Ivan presumably used the hexagonal setting, since they had c != a or b confusing I know Phil On 12 Aug 2010, at 00:42, xaravich ivan wrote: Hello Ray, You can contact the author of this paper. It seems they used denzo scalpack for R32. Ivan On Wed, Aug 11, 2010 at 8:53 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: If you cant import a file with symmetry labelled R32 but with a=b and alpha=beta = 90, and gamma = 120 then something is wrong - the symmetry checking looks at both name and cell.. or at least it used to.. The output mtz would have symmetry name changed to H32, but that is just a name - in each case the sym ops and cell should be h32 style.. Eleanor Ray Brown wrote: Hi, I have read all of the past messages about the confusion of H32 and R32 and I want to get the correct indexing sp that I can import the .sca file into CCP4.. I use DENZO and SCALEPACK in HKL2000. If you read the manual then it states that space group R32 should only be autoindexed by DENZO on a primitive lattice using the DENZO keyword H32. This indeed gives a primitive unit cell and not the hexagonal setting apparently demanded by CCP4 programs. What do you do next? It is possible in SCALEPACK to reindex the H32 primitive data into a rhombohedral hexagonal setting which SCALEPACK calls R32. Or course you cannot import this .sca file into CCP4. Why not? I can go into the .sca file and edit the header and change the R32 label to H32. Does this screw up the indexing? If anybody has successfully used DENZO/SCALEPACK/CCP4 in space group R32 then please tell me how to do it correctly. Cheers. Ray email ray-br...@att.net am0110-1.pdf
Re: [ccp4bb] process data in R32
Hi Ray, In HKL2000, by default (i.e. - without changing anything manually) for R32/H32, Denzo/Scalepack leads to a .sca file that has hexagonal unit cell parameters in the header but has the space group listed as R32. Scalepack2mtz in ccp4 does not like this mismatch so you have to simply change the space group name from R32 to H32 in the space group box in the Extra Information for MTZ File section of the scalepack2mtz gui and all should then be fine. good luck, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Wed, 11 Aug 2010, xaravich ivan wrote: Hello Ray, You can contact the author of this paper. It seems they used denzo scalpack for R32. Ivan On Wed, Aug 11, 2010 at 8:53 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: If you cant import a file with symmetry labelled R32 but with a=b and alpha=beta = 90, and gamma = 120 then something is wrong - the symmetry checking looks at both name and cell.. or at least it used to.. The output mtz would have symmetry name changed to H32, but that is just a name - in each case the sym ops and cell should be h32 style.. Eleanor Ray Brown wrote: Hi, I have read all of the past messages about the confusion of H32 and R32 and I want to get the correct indexing sp that I can import the .sca file into CCP4.. I use DENZO and SCALEPACK in HKL2000. If you read the manual then it states that space group R32 should only be autoindexed by DENZO on a primitive lattice using the DENZO keyword H32. This indeed gives a primitive unit cell and not the hexagonal setting apparently demanded by CCP4 programs. What do you do next? It is possible in SCALEPACK to reindex the H32 primitive data into a rhombohedral hexagonal setting which SCALEPACK calls R32. Or course you cannot import this .sca file into CCP4. Why not? I can go into the .sca file and edit the header and change the R32 label to H32. Does this screw up the indexing? If anybody has successfully used DENZO/SCALEPACK/CCP4 in space group R32 then please tell me how to do it correctly. Cheers. Ray email ray-br...@att.net
[ccp4bb] process data in R32
Hi, I have read all of the past messages about the confusion of H32 and R32 and I want to get the correct indexing sp that I can import the .sca file into CCP4.. I use DENZO and SCALEPACK in HKL2000. If you read the manual then it states that space group R32 should only be autoindexed by DENZO on a primitive lattice using the DENZO keyword H32. This indeed gives a primitive unit cell and not the hexagonal setting apparently demanded by CCP4 programs. What do you do next? It is possible in SCALEPACK to reindex the H32 primitive data into a rhombohedral hexagonal setting which SCALEPACK calls R32. Or course you cannot import this .sca file into CCP4. Why not? I can go into the .sca file and edit the header and change the R32 label to H32. Does this screw up the indexing? If anybody has successfully used DENZO/SCALEPACK/CCP4 in space group R32 then please tell me how to do it correctly. Cheers. Ray email ray-br...@att.net
