[ccp4bb] refine structure with mtz file in P212121 or P222?
Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei
Re: [ccp4bb] refine structure with mtz file in P212121 or P222?
Point 1) You don't need to reindex the data to change SG from P222 to P212121. Indexing and integration use the lattice type , and scaling the point group - not the space group. The only difference between the 2 space groups is that the odd axial reflections will be assent in P212121. Point 2) That is very very strange - if your solution is found for SG P212121 it is surprising if the refinement works better in P222! But check how the refinement and map generation is done. If the PDB file defines the SG as P212121 then maybe the refinement assumes the mtz file should also have that symmetry.. On 5 September 2014 16:54, Wei Shi wei.shi...@gmail.com wrote: Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei
Re: [ccp4bb] refine structure with mtz file in P212121 or P222?
As always, look at the unit cell packing of your alternative solutions. In all likelihood one of these two solutions from Phaser should pack sensibly in the unit cell, and the other will not. You may get some sort of quasi-reasonable-looking electron density out of the wrong solution initially, but usually not. It is possible that you indexed, integrated, and scaled in P222 and P212121, but if you do a full automated search in Phaser it will look for solutions in both space groups, and may have written out a solution in the same spacegroup both times. (Check the log file or PDB header.) Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 9/5/2014 11:54 AM, Wei Shi wrote: Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei
Re: [ccp4bb] refine structure with mtz file in P212121 or P222?
Thank you! Yes, the PDB file defines the SG as P212121. When I load pdb file from phaser (P222 mtz file as data and the solution is in P212121) into Phenix.refine, Phenix.refine automatically assumes that the space group is P212121. I am not sure in this case why using P222 mtz and P212121 mtz to do refinement would make a difference in the map. The difference is not very big but it's different for some atoms of the ligand Thank you! Best, Wei On Fri, Sep 5, 2014 at 3:40 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Point 1) You don't need to reindex the data to change SG from P222 to P212121. Indexing and integration use the lattice type , and scaling the point group - not the space group. The only difference between the 2 space groups is that the odd axial reflections will be assent in P212121. Point 2) That is very very strange - if your solution is found for SG P212121 it is surprising if the refinement works better in P222! But check how the refinement and map generation is done. If the PDB file defines the SG as P212121 then maybe the refinement assumes the mtz file should also have that symmetry.. On 5 September 2014 16:54, Wei Shi wei.shi...@gmail.com wrote: Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei
