Thank you, Nat! So, to process the data in space group P212121 in XDS generates the difference in the map compared to that processed in P222? Then, you would suggest to use the cns.hkl file from XDS using space group P222(?), and then do molecular replacement (try all possible in same pointgroup), and then do molecular replacement using the original mtz (from XDS, space group P222).... Thank you! I am just not quite sure why there is difference in density using two different mtz file....Thank you! Best, Wei On Fri, Sep 5, 2014 at 12:02 PM, Nathaniel Echols wrote:

On Fri, Sep 5, 2014 at 8:54 AM, Wei Shi wrote:

...

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.

Why did you run XDS again? You shouldn't need to do this, and if you really did reindex, that could explain why it's not working the way you expect. The MR solution already corresponds to the indexing in the P222 file - the only thing that is changing is what space group is being used internally. All you need to do is change the space group in the MTZ file to P212121, which you can also do in the reflection file editor. (Actually, you shouldn't even need to do that in order to run phenix.refine, since you can tell it to use P212121, and I suspect it will output the *_data.mtz file with the new space group which you can use from then on.) Don't reindex, don't change anything else.

-Nat