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Hi,<br>
<br>
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. <br>
<br>
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".<br>
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.<br>
<br>
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.<br>
<br>
Pavel.<br>
<br>
<br>
On 5/29/10 5:05 PM, Nathaniel Echols wrote:
<blockquote
cite="mid:AANLkTin1mHD9oXWKUk4n79m-42GFgaQC3O50BPTdfnVq@mail.gmail.com"
type="cite">On Sat, May 29, 2010 at 2:27 PM, Susan Tsutakawa <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:setsutakawa@lbl.gov">setsutakawa@lbl.gov</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.<br>
</blockquote>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>For now, I'd recommend using the FFT program in CCP4.</div>
<div><br>
</div>
<div>-Nat</div>
</div>
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