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Hi Omar,<br>
<br>
this is an old version. For latest features you need to use nightly
builds:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
I added electron scattering table option just a few months ago.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/10/15 2:20 PM, Omar Davulcu wrote:<br>
</div>
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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>
<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">
Pavel Afonine [<a class="moz-txt-link-freetext" href="mailto:pafonine@lbl.gov">mailto:pafonine@lbl.gov</a>]
<br>
<b>Sent:</b> Tuesday, February 10, 2015 2:07 PM<br>
<b>To:</b> Omar Davulcu; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] Calculating map with
electron scattering factors<o:p></o:p></span></p>
</div>
</div>
<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>
<div>
<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 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://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><o:p>�</o:p></span></p>
</div>
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