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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you so much, Elaine.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Kind Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Francesco<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Elaine Meng <meng@cgl.ucsf.edu>
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<b>Sent:</b> giovedì 14 gennaio 2021 17:28<br>
<b>To:</b> Francesco Papi <Francesco.Papi@iit.it><br>
<b>Cc:</b> Chimera <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Problem with electron density<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear Francesco,<o:p></o:p></p>
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<p class="MsoNormal">Probably you just need to use "vop cover" as described in these previous posts:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><<a href="https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html">https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html</a>><o:p></o:p></p>
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<p class="MsoNormal"><<a href="https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html">https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html</a>><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Details on the "vop cover" command:<o:p></o:p></p>
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<p class="MsoNormal"><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover</a>><o:p></o:p></p>
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<p class="MsoNormal">For future: the recommended address for questions is <a href="mailto:chimera-users@cgl.ucsf.edu">
chimera-users@cgl.ucsf.edu</a> (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question! <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I hope this helps,<o:p></o:p></p>
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<p class="MsoNormal">Elaine<o:p></o:p></p>
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<p class="MsoNormal">-----<o:p></o:p></p>
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<p class="MsoNormal">Elaine C. Meng, Ph.D. <o:p></o:p></p>
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<p class="MsoNormal">UCSF Chimera(X) team<o:p></o:p></p>
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<p class="MsoNormal">Department of Pharmaceutical Chemistry<o:p></o:p></p>
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<p class="MsoNormal">University of California, San Francisco<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">From: </span>
</b><span style="font-family:"Helvetica",sans-serif">Francesco Papi <<a href="mailto:Francesco.Papi@iit.it">Francesco.Papi@iit.it</a>></span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">Subject: Chimera: Problem with electron density</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">Date: </span>
</b><span style="font-family:"Helvetica",sans-serif">January 14, 2021 at 3:03:55 AM PST</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">To: </span>
</b><span style="font-family:"Helvetica",sans-serif">"<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>" <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dear Elaine,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in
an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera
mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thank you.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Regards, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Francesco Papi<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Francesco Papi, PhD</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">PostDoc<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Center for Nanotechnology Innovation@NEST<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="IT" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Istituto Italiano di Tecnologia</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="IT" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Piazza San Silvestro, 12</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="IT" style="font-size:11.0pt;font-family:"Calibri",sans-serif">56127 Pisa, Italy</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="IT" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Phone: +39 050 509 495</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="IT" style="font-size:11.0pt;font-family:"Calibri",sans-serif">E-mail:<span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="mailto:francesco.papi@iit.it"><span lang="IT" style="color:#954F72">francesco.papi@iit.it</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Skype: francesco.papi.89<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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