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<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>
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<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"> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<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; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] FEM mtz won't open in coot<o:p></o:p></span></p>
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<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>
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<p class="MsoNormal">On 5/8/14, 8:38 AM, R.M. Garavito wrote:<o:p></o:p></p>
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<p class="MsoNormal">Pavel, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Michael<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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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">****************************************************************</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 class="apple-style-span"><i><span style="font-size:9.0pt;font-family:Courier">603 Wilson Rd., Rm. 513 </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">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 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">Office: </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)
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 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>
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<br>
</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On May 8, 2014, at 11:13 AM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
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<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>
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<p class="MsoNormal">On 5/8/14, 8:01 AM, de Waal, Parker wrote:<o:p></o:p></p>
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<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>
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<pre><a 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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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">_______________________________________________<br>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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<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 href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre>
<pre><a 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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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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