[phenixbb] writing composite omit maps in .xplor

Pavel Afonine PAfonine at lbl.gov
Sat May 29 17:24:11 PDT 2010


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.


On 5/29/10 5:05 PM, Nathaniel Echols wrote:
> On Sat, May 29, 2010 at 2:27 PM, Susan Tsutakawa <setsutakawa at lbl.gov 
> <mailto:setsutakawa at lbl.gov>> 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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