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Hi Parker,<br>
<br>
can you please send me inputs so I can do comparisons myself and
provide comments?<br>
<br>
Usually, if FEM shows no density in places where there is density in
the original map, that missing density is either noise or model
bias. So it may not be a bad thing that you don't see it. This is
all I can say without looking at actual data, model and maps.<br>
<br>
Again, if you send me model and data, then I will provide detailed
comments.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/8/14, 11:38 AM, de Waal, Parker
wrote:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><span style="color:#1F497D">Thank you
everyone for the input! Using the manual loading method I
was able to view the new FEM map.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Unfortunately
it appears that FEM map is slightly worse than my original
map and is missing density in some areas. Has anyone
encountered this before?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Parker <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Pavel Afonine<br>
<b>Sent:</b> Thursday, May 08, 2014 12:28 PM<br>
<b>To:</b> R.M. Garavito; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] FEM mtz won't open in
coot<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Thanks
Michael,<br>
<br>
correct, as discussed this morning, auto-open in Coot will not
work for FEM maps, you need to load them manually. Thanks for
feedback!<br>
<br>
Pavel<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 5/8/14, 8:38 AM, R.M. Garavito wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Pavel, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Just to let you know, the auto-open
function works fine on the FEM mtz in the Mac version.
Makes a nice looking map which I am looking at now in the
context of earlier maps.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Michael<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">****************************************************************</span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">R.
Michael Garavito, Ph.D.</span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">Professor
of Biochemistry & Molecular Biology</span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
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<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">Michigan
State University </span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">East
Lansing, MI 48824-1319</span></i></span><span
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<p style="margin:0in;margin-bottom:.0001pt"><span
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style="font-size:9.0pt;font-family:Courier"> </span></i></span><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">(517)
355-9724 Lab: </span></i></span><span
class="apple-converted-space"><i><span
style="font-size:9.0pt;font-family:Courier"> </span></i></span><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">(517)
353-9125</span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">FAX: </span></i></span><span
class="apple-converted-space"><i><span
style="font-size:9.0pt;font-family:Courier"> </span></i></span><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">(517)
353-9334 Email: </span></i></span><span
class="apple-converted-space"><i><span
style="font-size:9.0pt;font-family:Courier"> </span></i></span><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier"><a
moz-do-not-send="true"
href="mailto:garavito@msu.edu">garavito@msu.edu</a></span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
class="apple-style-span"><i><span
style="font-size:9.0pt;font-family:Courier">****************************************************************</span></i></span><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><br>
<br>
</span><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On May 8, 2014, at 11:13 AM, Pavel
Afonine <<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>>
wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi
Parker,<br>
<br>
this requires loading map manually (not using
auto-open, as Nat pointed out):<br>
<br>
Start Coot -><br>
File -><br>
Open MTZ, mmCIF, fcf or phs -><br>
Choose file fem.mtz or whatever you called it, hit
Open -><br>
In popped menu "Column Label Assignment" choose:<br>
Amplitudes: FEM<br>
Phases: PHIFEM<br>
-> hit OK<br>
<br>
Contouring at 1sigma is universally good. Going down
to 0 should not change the appearance much.<br>
<br>
Pavel<o:p></o:p></p>
<div>
<p class="MsoNormal">On 5/8/14, 8:01 AM, de Waal,
Parker wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hello Everyone,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I’m having trouble opening the
map file generated by phenix.fem in coot. Each time
I try and load the .mtz file the follow error occurs
‘Failed to find any suitable F/phi columns in the
MTZ file’.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Dumping the mtz file I can see:<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Col Sort Min Max
Num % Mean Mean Resolution Type
Column<o:p></o:p></p>
<p class="MsoNormal">num order Missing
complete abs. Low High label<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> 1 NONE 0 33 0
100.00 12.1 12.1 114.15 3.31 H H<o:p></o:p></p>
<p class="MsoNormal"> 2 NONE 0 33 0
100.00 12.8 12.8 114.15 3.31 H K<o:p></o:p></p>
<p class="MsoNormal"> 3 NONE 0 137 0
100.00 51.4 51.4 114.15 3.31 H L<o:p></o:p></p>
<p class="MsoNormal"> 4 NONE 0.0 10551.1 22963
71.24 406.13 406.13 39.60 3.31 F 2mFoDFc<o:p></o:p></p>
<p class="MsoNormal"> 5 NONE -180.0 180.0 22963
71.24 0.98 89.81 39.60 3.31 P
PHI2mFoDFc<o:p></o:p></p>
<p class="MsoNormal"> 6 NONE 5.2 51589.8 0
100.00 1602.72 1602.72 114.15 3.31 F FEM<o:p></o:p></p>
<p class="MsoNormal"> 7 NONE -180.0 180.0 0
100.00 0.32 89.74 114.15 3.31 P PHIFEM<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">If someone could help me to
rename these columns to a coot friendly format so
that I would be greatly appreciative.
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Parker<o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times
New Roman","serif""><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>phenixbb mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://scanmail.trustwave.com/?c=129&d=t7Dr0wtxwUOeqd4xYqDpSfgkuCoj8ZQxnCe0qvjCOQ&u=http%3a%2f%2fphenix-online%2eorg%2fmailman%2flistinfo%2fphenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre>
</blockquote>
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style="font-size:12.0pt;font-family:"Times New
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<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif"">_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://scanmail.trustwave.com/?c=129&d=t7Dr0wtxwUOeqd4xYqDpSfgkuCoj8ZQxnCe0qvjCOQ&u=http%3a%2f%2fphenix-online%2eorg%2fmailman%2flistinfo%2fphenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></span></p>
</div>
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style="font-size:12.0pt;font-family:"Times New
Roman","serif""><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>phenixbb mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://scanmail.trustwave.com/?c=129&d=t7Dr0wtxwUOeqd4xYqDpSfgkuCoj8ZQxnCe0qvjCOQ&u=http%3a%2f%2fphenix-online%2eorg%2fmailman%2flistinfo%2fphenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre>
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