<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body 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<br>
<br>
<div class="moz-cite-prefix">On 9/7/14 2:38 PM, Tanner, John J.
wrote:<br>
</div>
<blockquote
cite="mid:00B8915F-2FB5-4F2E-90D1-A05B57263250@missouri.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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">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 class="Apple-interchange-newline">
<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 class="moz-cite-prefix">On 9/7/14 11:14 AM, Tanner,
John J. wrote:<br>
</div>
<blockquote
cite="mid:B335D1E2-5277-4ED0-A4B9-AB1540CD08FA@missouri.edu"
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 apple-content-edited="true">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space; ">
<span class="Apple-style-span"
style="border-collapse: separate; font-family:
Helvetica; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2;
text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; font-size:
medium; ">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space; ">
<span class="Apple-style-span"
style="border-collapse: separate;
font-family: Helvetica; font-style: normal;
font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto;
text-indent: 0px; text-transform: none;
white-space: normal; widows: 2;
word-spacing: 0px;
-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; font-size:
medium; ">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<span class="Apple-style-span"
style="border-collapse: separate;
font-family: Helvetica; font-style:
normal; font-variant: normal;
font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2;
text-align: -webkit-auto; text-indent:
0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect:
none; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px;
font-size: medium; ">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;
">
John J. Tanner, PhD<br>
Professor of Biochemistry and�Director
of Graduate Admissions and Recruitment</div>
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;
">
Professor of Chemistry (Joint
Appointment)</div>
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;
">
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">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">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a><br>
<br>
</div>
</span></div>
</span></div>
</span></div>
</div>
</blockquote>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>