On Fri, Jul 15, 2011 at 1:27 PM, Yuri
I collected data on a new crystal, indexed, scaled (2.75 A), ran molecular replacement (40% homologue) and found a solution. I did some building got a new model, did an initial refinement (using my .sca file, not data.mtz from mol rep). I then ran phase_and_build with density modification. The new maps look a lot better and I am able to see some residues I was not able to place before. I did some more building and I am ready to refine. What should I use as experimental data? phase and_build gave me a .mtz file with amplitudes (no I) and "experimental phase" coeeficients (HLAM. HLBM,...)
You should use the file ending in _data.mtz output by phenix.refine after the initial refinement - this contains your amplitudes and the R-free flags that phenix.refine generated, and it's essential that you continue to use these. What did you use as input for phase_and_build? It will create its own R-free flags if none are found in the input file, which in this case would be bad. (You definitely should not use the Hendrickson-Lattman coefficients output by phase_and_build - only experimental phases from AutoSol, etc. Unfortunately our software is not [yet] smart enough to tell the difference, since they're all the same in the MTZ files.) -Nat