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Hello Wei,<br>
<br>
Maps you see in Coot are three-dimensional functions calculated on
the grid. These functions are the finite resolution and finite
quality images of electron (or nuclear, depending experiment)
density in the crystal. They are calculated as a Fourier transform
of Fourier map coefficients. In most cases these Fourier map
coefficients are {2mFobs-DFmodel, PhiFmodel} and {mFobs-DFmodel,
PhiFmodel}, that are complex numbers. Refinement programs like
Refmac or phenix.refine output these map coefficients in MTZ
formatted files, or you can calculated them given Fobs and atomic
model using standalone programs, such as phenix.maps for instance.<br>
<br>
Back to you original question: 'Create maximum entropy map' utility
expected from you one of these MTZ files.<br>
<br>
Hope this helps,<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 9/20/14 10:41 AM, Wei Shi wrote:<br>
</div>
<blockquote
cite="mid:CA+Sz7q5aCQBJiVYpkd_pejnfRRKcfLXFpsC18DS_NeLdE4Oyng@mail.gmail.com"
type="cite">
<div dir="ltr">The mtz file I loaded is from Phenix ->
Reflection file editor with default settings using the cns.hkl
file from xds. I am not sure how to get the MTZ with Fourier map
coefficients. Thank you!<br>
<br>
Best, <br>
Wei <br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sat, Sep 20, 2014 at 12:39 PM, Pavel
Afonine <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Most likely this is
because you loaded MTZ with with no Fourier map
coefficients.<span class="HOEnZb"><font color="#888888"><br>
Pavel</font></span>
<div>
<div class="h5"><br>
<br>
<div>On 9/20/14 8:39 AM, Wei Shi wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Thank you so much! Is 'Create maximum
entropy map' in the latest nightly build that
could create the omit map you guys suggested? I
was trying to run it but got the error message 'No
column labels specified'. In the columns labels it
shows '---' and don't give me any option to
change... I just loaded my mtz file and the
ligand-free pdb file and left all other settings
as default. Thank you so much! <br>
<br>
Best, <br>
Wei </div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Sep 17, 2014 at
2:39 AM, Dale Tronrud <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:detBB@daletronrud.com"
target="_blank">detBB@daletronrud.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"><br>
I don't believe I said he was the first.
He did develop an<br>
implementation which has proven useful to a
large number of people.<br>
<span><font color="#888888"><br>
Dale<br>
</font></span><span><br>
On 9/16/2014 8:52 PM, Nathaniel Echols
wrote:<br>
> On Tue, Sep 16, 2014 at 11:36 AM, Dale
Tronrud <<a moz-do-not-send="true"
href="mailto:detBB@daletronrud.com"
target="_blank">detBB@daletronrud.com</a><br>
</span>
<div>
<div>> <mailto:<a
moz-do-not-send="true"
href="mailto:detBB@daletronrud.com"
target="_blank">detBB@daletronrud.com</a>>>
wrote:<br>
><br>
> This sounds like Bricogne's
maximum entropy maps.<br>
><br>
><br>
> Maybe I'm misunderstanding this
reference, but I don't think Bricogne<br>
> was the first person to come up with
the idea:<br>
><br>
> <a moz-do-not-send="true"
href="https://www.researchgate.net/publication/232761305_Electron_density_images_from_imperfect_data_by_iterative_entropy_maximization"
target="_blank">https://www.researchgate.net/publication/232761305_Electron_density_images_from_imperfect_data_by_iterative_entropy_maximization</a><br>
><br>
> which I think is just an extension of
the application to X-ray astronomy<br>
> described by Gull & Daniel
(1978).<br>
><br>
> -Nat<br>
</div>
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