Hi Jason, I am a little puzzled about the one chain ("A"?) in overall_best_edited.pdb. This file should be very similar to your input pdb file (I think overall_best.pdb in your case). However in any case the output PDB files from iterative_build_omit have no significance, and should be ignored. You use your input PDB file as a comparison with the map. So usually you run an iterative-build omit map to make sure that your model is not biasing your map in any serious way. I would recommend running regular autobuild (rebuild_in_place=false first usually, then rebuild_in_place=True) to get the best model you can. If you have some uncertainty about model bias, then make the iterative-build omit map as you have, and use that as a reference to check whether your model is ok. If there are aspects of your model that the iterative_build omit map shows to be clearly incorrect, then you might want to redo them. If you want to be extra-sure about your model and you have experimental phases, you can run autobuild starting with your experimental phases (no model) and specify an iterative-build omit map...in this case your final map is totally unbiased by your model-building, but is nevertheless greatly improved over your starting map. You will nearly always get the best map, however, by carrying out a regular (not omit) autobuild run. I hope that helps! All the best, Tom T

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Hello everyone,

I used default setting in phenix and made an iterative-build omit map (it took 3 days!!!). Input: a pdb file (6 identical chains in AU); an mtz file output: a resolve_composite_map.mtz; an overall_best_edited.pdb

questions:

1) There is only one chain in overall_best_edited.pdb, the resolve_composite_map.mtz clearly indicates there are 6 chains in AU.

2) What's the next step for me after obtaining resolve_composite_map.mtz? a) use phenix.refine to do refinement? if this is the case, what files should I use? b) use phenix.assign_sequence to assign sequence to resolve_composite_map.mtz? c) something else?

Thanks in advance.

Jason

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