<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Wangshu,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>This certainly seems to be a bug. This structure is shown correctly in ChimeraX, so depending on your needs you could use that. Also, it is shown correctly in Chimera if you use the mmCIF version. You can do that by using File->Fetch By ID and choosing “PDB (mmCIF)” as the database and then typing in 3lr2. Lastly, you can manually fix the PDB version by adding the missing peptide bonds by entering the following commands:</div><div class=""><br class=""></div><div class=""><div class="">bond :42.a@c :43.a@n</div></div><div class=""><div class="">bond :47.a@c :48.a@n</div></div><div class=""><div class="">bond :51.a@c :52.a@n</div></div><div class=""><div class=""><div class="">bond :125.a@c :126.a@n</div></div></div><div class=""><div class="">bond :47.b@c :48.b@n</div><div class=""></div></div><div class=""><div class="">bond :48.b@c :49.b@n</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Thanks for reporting the problem. I will work on a fix.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""></div></div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On Oct 31, 2017, at 3:18 PM, Wangshu Jiang <<a href="mailto:wangshu.jiang@icm.uu.se" class="">wangshu.jiang@icm.uu.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Dear Chimera Support,
<div class="">I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken,
both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB
instead of manually deleting by coot just from ‘eyeballing'. </div>
<div class=""><br class="">
</div>
<div class="">Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!</div>
<div class=""><br class="">
</div>
<div class="">Best Regards,</div>
<div class="">
<div class="">
<div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
Wangshu Jiang<br class="">
<br class="">
PhD student<br class="">
Dept Cell and Molecular Biology<br class="">
BMC Box 596<br class="">
Husargatan 3<br class="">
751 24 Uppsala Sweden</div>
</div>
<br class="">
</div>
<div class=""><span id="cid:0D42E809-5937-4AC1-83FB-07A00C355333"><BrokenPeptide.png></span></div>
<div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Wangshu Jiang<br class="">
<br class="">
PhD student<br class="">
Dept Cell and Molecular Biology<br class="">
BMC Box 596<br class="">
Husargatan 3<br class="">
751 24 Uppsala Sweden</div>
</div>
<br class="">
</div>
_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>