[phenixbb] An easier explanation of the regions in omit map

xaravich ivan xaravich.ivan at gmail.com
Mon May 17 10:53:04 PDT 2010

Hi Nat,
So I have quite a few regions build by the SA_omit map of phenix. But How do
I go about looking at these maps. What am I looking for here. Should I look
at the regions where the occupancy was set zero in all these outputs and
find if I could build some thing from one of the maps? I guess I am asking,
How do I use this information to move forward in refinement? There are 24
regions map and .pdb output in the /OMIT directory.


On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Fri, May 14, 2010 at 5:40 PM, xaravich ivan <xaravich.ivan at gmail.com>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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