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Could you please try latest Phenix from nightly builds or send me
files off-list and I will try right now?<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/22/14 3:22 PM, Murpholino Peligro
wrote:<br>
</div>
<blockquote
cite="mid:CAMdBu0U_+MSAGY3FTKhyedj0=hojc1RZXmTx9G1KKQz61Mm5Aw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>I also can see something like that...<br>
</div>
<a moz-do-not-send="true"
href="https://www.dropbox.com/s/lfd2sz44b4yzu5c/water19.png?dl=0">https://www.dropbox.com/s/lfd2sz44b4yzu5c/water19.png?dl=0</a><br>
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<div><br>
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<div>purple is FEM and blue is normal map.<br>
<br>
<br>
</div>
<div><br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">2014-09-09 1:36 GMT-05:00 Pavel Afonine
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi John,<br>
<br>
thanks for feedback, this is very valuable as I'm still
gaining experience with FEM and tuning the protocol based
on it.<br>
<br>
I can't tell what exactly happens unless I have data and
model files and can reproduce the map you get. Would mind
sharing the files off list so I can have a closer look?<br>
<br>
Thanks!<br>
Pavel
<div>
<div class="h5"><br>
<br>
<div>On 9/7/14 2:38 PM, Tanner, John J. wrote:<br>
</div>
</div>
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<blockquote type="cite">
<div>
<div class="h5"> Well, this is embarrassing...the
assign label window was hiding behind the graphics
window.
<div><br>
</div>
<div>Now that I do see the FEM, I have an
observation about the FEM. Although the FEM is
providing an informative assessment of the protein
and bound ligands, the assessment of water is a
little strange. There are several water molecules
that have strong 2Fo-Fc density but absolutely
zero FEM density. Even if I contour the FEM down
to the lowest possible value (0.09 sigma in this
case), I still see no FEM density on these waters.
The waters in question have good hydrogen
bonding to the protein and acceptable B-factors
(26-30 Ang^2). These are waters that I would
normally keep in my final model. Has anyone else
seen this behavior? </div>
<div><br>
</div>
<div>Some examples are posted here:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://faculty.missouri.edu/%7Etannerjj/FEMwaters/FEMwaters.html"
target="_blank">http://faculty.missouri.edu/~tannerjj/FEMwaters/FEMwaters.html</a></div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div>
<div>On Sep 7, 2014, at 2:51 PM, Pavel Afonine
wrote:</div>
<br>
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">Hi
John,<br>
<br>
it does not open via Auto Open MTZ.<br>
<br>
start Coot then<br>
<br>
File -> Open MTZ, mmCIF, fcf or phs
-> the choose FEM,PHIFEM (there are two
Fourier maps in this file : FEM and usual
2mFo-DFc).<br>
<br>
Pavel<br>
<br>
<div>On 9/7/14 11:14 AM, Tanner, John J.
wrote:<br>
</div>
<blockquote type="cite"> Has anyone had
problems reading feature enhanced map
mtz files into coot? I made an FEM on a
linux computer with phenix.fem, which
created an mtz file:
<div><br>
</div>
<div>
<div>-rw-r--r-- 1 tannerjj tanner
10760960 Sep 7 12:21 fem.mtz</div>
</div>
<div><br>
</div>
<div>As you can see, the mtz file is not
empty. The fem job appeared to have
ended normally, since the last line in
the out file is</div>
<div><br>
</div>
<div>FEM loop: done so far: 100%Time:
3112.3967</div>
<div><br>
</div>
<div>However, when I read this mtz into
coot, the map does not appear. There
is no error message from coot. I tried
autoinput mtz and read mtz. I'm using
coot on a mac. I have not tested
with coot on Linux.</div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Jack Tanner</div>
<div><br>
</div>
<div><br>
</div>
<br>
<br>
<div>
<div style="word-wrap:break-word"> <span
style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium">
<div style="word-wrap:break-word">
<span
style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium">
<div
style="word-wrap:break-word">
<span
style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium">
<div
style="word-wrap:break-word">
John J. Tanner, PhD<br>
Professor of
Biochemistry
and Director of Graduate
Admissions and
Recruitment</div>
<div
style="word-wrap:break-word">
Professor of Chemistry
(Joint Appointment)</div>
<div
style="word-wrap:break-word">
University of
Missouri-Columbia<br>
125 Chemistry Building<br>
Columbia, MO 65211<br>
email: <a
moz-do-not-send="true"
href="mailto:tannerjj@missouri.edu" target="_blank">tannerjj@missouri.edu</a><br>
phone: 573-884-1280<br>
fax: 573-882-2754<br>
<a
moz-do-not-send="true"
href="http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html"
target="_blank">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a><br>
<br>
</div>
</span></div>
</span></div>
</span></div>
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