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<p class="MsoNormal"><span style="color:#1F497D">Hi Pavel,<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">Thanks for getting back to me. I’m running Phenix version 1.9, build 1692. When I run phenix.maps to generate a maps.params file, I don’t see electron as an option for scattering_table. I do see the other
four options, though.<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">When I run phenix.fmodel as you suggested, but substituting the actual name of the pdb file, I get an error message saying:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Sorry: Not a possible choice for scattering_table: electron (command line argument, line 1)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> Possible choices are:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> wk1995<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> it1992<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> *n_gaussian<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> neutron<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">While it seemed pretty straightforward, is it possible that I haven’t installed Phenix properly?<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">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Omar<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"> Pavel Afonine [mailto:pafonine@lbl.gov]
<br>
<b>Sent:</b> Tuesday, February 10, 2015 2:07 PM<br>
<b>To:</b> Omar Davulcu; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Calculating map with electron scattering factors<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">Hi Omar,<br>
<br>
electron scattering table is fully supported. In phenix.maps it is <br>
<br>
scattering_table = wk1995 it1992 *n_gaussian neutron electron<br>
<br>
But if you just want to compute a Fourier map from a PDB file then this is more straightforward:<br>
<br>
phenix.fmodel model.pdb high_res=2.3 scattering_table=electron<br>
<br>
You need to have a reasonably recent version of Phenix for this.<br>
<br>
Pavel<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 2/10/15 1:57 PM, Omar Davulcu wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi, everyone.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Probably a silly question, but here goes…<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I’m trying to calculate a simulated map around a set of coordinates using the electron scattering table. Phenix.maps doesn’t appear to allow selection of that particular scattering table.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I noticed that phenix.refine allows me to select that table and I thought I would set the number of macro cycles to 0 and turn off all the refinement options and produce a map that way. I thought I would generate the structure factors
needed as input with phenix.fmodel, but that also doesn’t allow selection of the electron scattering table.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">So, my (na�ve) question is: what am I doing wrong? Is there a way I can calculate this map in phenix? Any help would be greatly appreciated.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thanks much!<o:p></o:p></p>
<p class="MsoNormal">Omar Davulcu<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <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 href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre>
<pre><a href="http://phenix-online.org/mailman/listinfo/phenixbb">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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