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Dear Elaine,
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<div class="">Thank you so much for your help! The commands work like a charm:-) I am happy that you did not regard my question as a Halloween prank. Very grateful to have support from you guys so fast!</div>
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<div class="">I will have a look at your new program ChimeraX. May I ask if I install ChimeraX on my mac, does it mean it will replace my previous Chimera or can they exist at the same time?</div>
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<div class="">Thanks again and hope you have a lovely day!</div>
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<div class="">Best Regards, <br class="">
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Wangshu Jiang<br class="">
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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>
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<div class="">On 31 Oct 2017, at 23:58, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
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<div class="PlainText">Dear Wangshu Jiang,<br class="">
I’m not sure exactly what’s going on with 3LR2, but you can add the missing bonds, for example with commands (also attached as a command file for your convenience):<br class="">
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bond :42.a@c :43.a@n<br class="">
bond :47.a@c :48.a@n<br class="">
bond :51.a@c :52.a@n<br class="">
bond :125.a@c :126.a@n<br class="">
bond :47.b@c :48.b@n<br class="">
bond :48.b@c :49.b@n<br class="">
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I think I got all of the breaks. Hey, seems like this a good protein for Halloween (spider silk)! :-)<br class="">
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Sorry for the hassle. Our newer program ChimeraX doesn’t have this problem with 3LR2, but it handles alternate locations differently. <span class="Apple-converted-space"> </span><br class="">
I hope this helps,<br class="">
Elaine<br class="">
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Elaine C. Meng, Ph.D. <span class="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="">
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> 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:<br class="">
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> Dear Chimera Support,<br 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'.<span class="Apple-converted-space"> </span><br class="">
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> 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!<br class="">
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> Best Regards,<br class="">
> Wangshu Jiang<br class="">
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> PhD student<br class="">
> Dept Cell and Molecular Biology<br class="">
> BMC Box 596<br class="">
> Husargatan 3<br class="">
> 751 24 Uppsala Sweden<br class="">
><span class="Apple-converted-space"> </span><br class="">
> <BrokenPeptide.png><br class="">
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<span id="cid:52D5378182FECD468B61710BE7CB9902@user.uu.se"><bondit.cmd></span></div>
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