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 >> > >
