Hi,

I think this is a good option-candidate for phenix.maps. Currently phenix.maps can create a variety of maps and can output them in X-plor or MTZ format.

Yes, generating an omit map is missing in phenix.maps as an explicit option. But you can just manually omit the region in question and compute a Kick Map. It is a simple alternative to "SA omit map" or "Iterative Build omit map".
Or alternatively: a) omit the region in question, b) do some refinement, c) after refinement phenix.refine will give your the omit maps or you can just use phenix.maps to compute the map. I this this is the complete solution for what you want.

For more information about phenix.maps just type this command in the command line and hit Enter - the quick manual will be printed to the screen.

Pavel.

On 5/29/10 5:05 PM, Nathaniel Echols wrote:

On Sat, May 29, 2010 at 2:27 PM, Susan Tsutakawa <[email protected]> wrote:

Continuing the conversation on looking at Phenix maps in pymol, what is the best way to generate .xplor maps in Autobuild. I would like to generate a figure in pymol with an omit map. I wasn't able to find documentation explicitly stating how this can be done.

The GUI generates XPLOR maps automatically; otherwise, I don't think there's a simple mechanism in Phenix for this right now. I started working on a script for this but got sidetracked - I'll see if I can dust off the code and get something working for the next release.

For now, I'd recommend using the FFT program in CCP4.

-Nat
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