Re: [phenixbb] Looking at omit maps in coot

Thanks Nat, Its the latest version I downloaded less than a week back. It is in Mac OS X. I am using GUI. Basically I have made most of the model and as it was from Molecular Replacement it still has that high R free and I am sure that parts of the model has that bias and does not fit niceley. I deleted those regions and used SA_omit map in phenix GUI. It made a composite omit map by default. and it has made those number of regions of pdb and mtz files. The coot is distinctly indicating that it could not open the map/mtz. even when I try to open from phenix or separately from command line. Thanks, Ivan On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols wrote:

On Fri, May 14, 2010 at 5:40 PM, xaravich ivan wrote:

...

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

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