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<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Dear Elaine,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy">many thanks for your detailed information and sorry for my delayed answer- I was out of duties.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy">Since I will need soon to use properly the software, I have looked in details the links you sent me; nevertheless I think
I will come back to you for some specific question in the near future.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy">Best regards<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy">Emanuele<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size:10.0pt;font-family:Arial;color:navy"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><b><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma;font-weight:bold">Von:</span></font></b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"> Elaine Meng [mailto:meng@cgl.ucsf.edu]
<br>
<b><span style="font-weight:bold">Gesendet:</span></b> Freitag, 2. Oktober 2015 19:00<br>
<b><span style="font-weight:bold">An:</span></b> <st1:PersonName w:st="on">Coci, Emanuele</st1:PersonName><br>
<b><span style="font-weight:bold">Cc:</span></b> chimera-users@cgl.ucsf.edu List<br>
<b><span style="font-weight:bold">Betreff:</span></b> 3D-visualization of protein chain and mutation</span></font><o:p></o:p></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="2" face="Helvetica"><span style="font-size:10.0pt;
font-family:Helvetica">From: "<st1:PersonName w:st="on">Coci, Emanuele</st1:PersonName>" <<a href="mailto:Emanuele.Coci@akh-celle.de">Emanuele.Coci@akh-celle.de</a><<a href="mailto:Emanuele.Coci@akh-celle.de">mailto:Emanuele.Coci@akh-celle.de</a>>><br>
Date: Friday, October 2, 2015 at 8:54 AM<br>
Subject: 3D-visualization of protein chain<br>
<br>
Deat Chimera team,<br>
my name is Emanuele Coci, MD PhD.<br>
<br>
I would kindly ask you for help about Chimera software in solving the following technical issue. I want to visualize the 3D-structure of a mutated protein chain.<br>
<br>
Which of the chimera tools is more indicated to visualize the 3D structure?<br>
Is the toll open source?<br>
Which software do I need to download the tool on my PC : JAVA, …?<br>
<br>
Best regards and many thanks in advance?<br>
Emanuele Coci<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Dear Emanuele Coci,<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Chimera is a free download for any noncommercial use (research, education, …) and is available for Windows, Mac, and Linux. You should not have to download any other
software to use it. All you need is a reasonably modern computer. See Chimera homepage and download links:<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="http://www.rbvi.ucsf.edu/chimera/index.html">http://www.rbvi.ucsf.edu/chimera/index.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="http://www.rbvi.ucsf.edu/chimera/download.html">http://www.rbvi.ucsf.edu/chimera/download.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">I’ve CC’d
<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> — that is the proper address for user questions.<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">There are many possible styles of displaying a protein, and you have to use your own judgement and artistic taste to decide which style is best for what you want to
see for yourself or show to others. There are several step-by-step tutorials for learning how to use Chimera, including “getting started” for beginners and some example image tutorials:<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html">http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">For showing a mutation, the first thing you could do is just show the location of that amino acid on the structure (without mutating it), for example coloring it differently
than the rest of the structure. It may be helpful to show the sequence of the protein so that you can identify the correct position (Chimera menu: Favorites… Sequence). You can choose a residue with the mouse in the sequence window, which will automatically
select-highlight it in the structure.<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Secondly, you could try “mutating” that residue computationally. This could be done with the Rotamers tool (in menu under Tools… Structure Editing) or the “swapaa”
command. There is an example of using the Rotamers tool in the “Structure Analysis and Comparison” tutorial:<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html</a>><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">However, Chimera will not predict any larger-scale changes in the structure from the mutation or calculate changes in stability or affinity. It will only change the
sidechain and not move anything else. You can use Rotamers to analyze the H-bonds and clashes (bad contacts) of different conformations of the sidechain, which may allow you to hypothesize whether the mutation would be disruptive to the stability or interactions
of the protein.<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">I hope this helps,<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Elaine<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">-----<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Elaine C. Meng, Ph.D. <o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Department of Pharmaceutical Chemistry<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">University of California, San Francisco<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><o:p> </o:p></span></font></p>
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