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<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Times New Roman",serif">HI Elaine,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Times New Roman",serif">I have docked the relevant atomic structure in the computed density map of C6 symmetry. I will now need to generate another 5 copies of the atomic structure to fit in the
density envelope. And I was looking for the complete command. Let me know what will be the command.
<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:#006FC9">Anindito Sen. Ph.D</span></b><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
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</span><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:#006FC9">Texas A&M University </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Reply-To: </b>"chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu><br>
<b>Date: </b>Friday, January 21, 2022 at 12:30 PM<br>
<b>To: </b>"Sen, Anindito" <andysen@tamu.edu><br>
<b>Cc: </b>"chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [Chimera-users] Making copies of an atomic structure and fit in the map<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="pfptpreheader1"><span style="font-size:1.0pt;color:white">Hi Anindito. We couldn't say what the "sym" command would be without knowing what information is in the structure file (PDB or mmCIF). If there is not symmetry information
in the file then you have to specify it in the command instead, which </span></span><span style="font-size:1.0pt;color:white">ZjQcmQRYFpfptBannerStart</span>
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<pre style="white-space:pre-wrap;word-wrap: break-word"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Hi Anindito.<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">We couldn't say what the "sym" command would be without knowing what information is in the structure file (PDB or mmCIF). If there is not symmetry information in the file then you have to specify it in the command instead, which can be difficult.<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">However, maybe what you really want is "fitmap" with symmetrical fitting (instead of making copies with "sym" first). In that case your density map must have symmetry information. See "fitmap" help and video:<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html*symmetric__;Iw!!KwNVnqRv!UOhSQHX1qxC6PyIRYSi9YTK5pEIbS8YjJ4J4Hck_5Zqx8j0ahi9SHpEVmVEkrEQ$ ><o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/__;!!KwNVnqRv!UOhSQHX1qxC6PyIRYSi9YTK5pEIbS8YjJ4J4Hck_5Zqx8j0ahi9SHpEVZqAfnpQ$ ><o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">I hope this helps,<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Elaine<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">-----<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Elaine C. Meng, Ph.D. <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">UCSF Chimera(X) team<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Department of Pharmaceutical Chemistry<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">University of California, San Francisco<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Begin forwarded message:<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> From: "Sen, Anindito" <andysen@tamu.edu><o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Subject: Making copies of an atomic structure and fit in the map<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Date: January 20, 2022 at 4:08:11 PM PST<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> To: Chimera-users <chimera-users-bounces@cgl.ucsf.edu><o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Dear All,<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> What will be the correct complete command (sym) for making copies of an atomic structure and symmetrize them to dock in the relevant density map.<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Stay safe & Regards<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Anindito Sen. Ph.D<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Microscopy and Imaging Center <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Texas A&M University <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> 301 Old Main Dr<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> College Station, TX 77843-2257<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> <o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Office: ILSB Room 1133<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> Tel. 979-458-9881<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> fax: 979-847-8933<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif">> http://microscopy.tamu.edu<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></pre>
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