Again this is pretty novice and I would apologize in advance.
I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map.
I am pretty clueless.
Some clarification:
1. Which version of Phenix, and which platform?
2. GUI or command-line?
3. If you're really making a composite omit map (as opposed to a simple omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and stick to the original.
One common problem is that on Mac, if you try to open the MTZ file in Coot (using the "Open MTZ", not auto-open), it will open a window to choose column labels in the file, but it opens *behind* the main window, which you need to move to the side temporarily.
-Nat