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Hi Eric,</div>
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Actually, even short sequences do get a tilt - please see attached images from Chimera and the imported model in Blender (same tilt).</div>
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<font size="2">Best regards</font></p>
<p style="padding:0px; margin-top:1em; margin-right:0px; margin-left:0px; background-color:rgb(255,255,255)">
<font size="2">Andreas Göransson<br style="padding:0px; margin:0px">
PhD Student<br style="padding:0px; margin:0px">
ITN<br style="padding:0px; margin:0px">
Linköping University<br style="padding:0px; margin:0px">
Phone +46 11 36 30 79</font></p>
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<font size="2">Visiting address: Hus Kopparhammaren, G518, </font><span style="font-size:small">Campus Norrköping</span></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Från:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Skickat:</b> den 25 november 2020 20:08<br>
<b>Till:</b> Andreas Göransson <andreas.c.goransson@liu.se><br>
<b>Kopia:</b> chimerax-users <chimerax-users@cgl.ucsf.edu><br>
<b>Ämne:</b> Re: [chimerax-users] Build DNA structure in Chimera X</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Andreas,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>You must be using a very long sequence of base pairs. To my eye, a 100-bp nucleic acid structure built by Chimera looks pretty straight. I would guess that any slight bend/tilt is
due to cumulative roundoff error in the transformation matrix as it places one base pair relative to the next. If you need something absolutely straight, two possibilities are: 1) minimize the structure afterward [steepest descent steps only; conjugate gradient
will take forever], or 2) use another nucleic-acid builder, such as the "nab" program (<b class="">n</b>ucleic
<b class="">a</b>cid <b class="">b</b>uilder) from AmberTools (<a href="http://ambermd.org" class="">ambermd.org</a>).</div>
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<div class="">--Eric</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Nov 25, 2020, at 10:12 AM, Andreas Göransson <<a href="mailto:andreas.c.goransson@liu.se" class="">andreas.c.goransson@liu.se</a>> wrote:</div>
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<span class="">Hi Elaine, and thank you for your fast reply! </span></div>
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Yes, I suspected that it was not available, just wanted to make sure that I got it right. By the way, do you happen to know why B-DNA built in Chimera has a slight tilt/rotation, i.e. it is not exactly vertical? Sometimes one wants to import the structure into
3D software like Blender to make further processing and animation possible and then it would have been convenient to have it perfectly vertical. </div>
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<font size="2" class="">Best regards</font></div>
<p class="" style="margin:1em 0px 0px; padding:0px; background-color:rgb(255,255,255)">
<font size="2" class="">Andreas Göransson<br class="" style="padding:0px; margin:0px">
PhD Student<br class="" style="padding:0px; margin:0px">
ITN<br class="" style="padding:0px; margin:0px">
Linköping University<br class="" style="padding:0px; margin:0px">
Phone +46 11 36 30 79</font></p>
<p class="" style="margin:1em 0px 0px; padding:0px; background-color:rgb(255,255,255)">
<font size="2" class="">Visiting address: Hus Kopparhammaren, G518, </font><span class="" style="font-size:small">Campus Norrköping</span></p>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">Från:</b><span class="x_Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">
<b class="">Skickat:</b><span class="x_Apple-converted-space"> </span>den 25 november 2020 17:44<br class="">
<b class="">Till:</b><span class="x_Apple-converted-space"> </span>Andreas Göransson <<a href="mailto:andreas.c.goransson@liu.se" class="">andreas.c.goransson@liu.se</a>><br class="">
<b class="">Kopia:</b><span class="x_Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><span class="x_Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class="">
<b class="">Ämne:</b><span class="x_Apple-converted-space"> </span>Re: [chimerax-users] Build DNA structure in Chimera X</font>
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<div class="x_PlainText">Hi Andreas,<br class="">
ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when.<br class="">
Best,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <span class="x_Apple-converted-space"> </span><br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<br class="">
> On Nov 25, 2020, at 2:37 AM, Andreas Göransson <<a href="mailto:andreas.c.goransson@liu.se" class="">andreas.c.goransson@liu.se</a>> wrote:<br class="">
><span class="x_Apple-converted-space"> </span><br class="">
> Dear Chimera X users,<br class="">
><span class="x_Apple-converted-space"> </span><br class="">
> I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?<br class="">
><span class="x_Apple-converted-space"> </span><br class="">
> THanks in advance,<br class="">
> Andreas<br class="">
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