<div dir="ltr"><div><div>I also can see something like that...<br></div><a href="https://www.dropbox.com/s/lfd2sz44b4yzu5c/water19.png?dl=0">https://www.dropbox.com/s/lfd2sz44b4yzu5c/water19.png?dl=0</a><br></div><div><br></div><div>purple is FEM and blue is normal map.<br><br><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-09 1:36 GMT-05:00 Pavel Afonine <span dir="ltr"><<a 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></div><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 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">
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<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 href="mailto:tannerjj@missouri.edu" target="_blank">tannerjj@missouri.edu</a><br>
phone: 573-884-1280<br>
fax: 573-882-2754<br>
<a 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>
</div>
</blockquote>
</div>
</blockquote>
</div>
<br>
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