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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: [log in to unmask] 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