[Chimera-users] problem with showing broken peptide after residues with alternative conformation

Wangshu Jiang wangshu.jiang at icm.uu.se
Tue Oct 31 15:18:12 PDT 2017


Dear Chimera Support,
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'.

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!

Best Regards,
Wangshu Jiang

PhD student
Dept Cell and Molecular Biology
BMC Box 596
Husargatan 3
751 24 Uppsala Sweden

[cid:0D42E809-5937-4AC1-83FB-07A00C355333]
Wangshu Jiang

PhD student
Dept Cell and Molecular Biology
BMC Box 596
Husargatan 3
751 24 Uppsala Sweden

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20171031/49e3da70/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BrokenPeptide.png
Type: image/png
Size: 198624 bytes
Desc: BrokenPeptide.png
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20171031/49e3da70/attachment-0001.png>


More information about the Chimera-users mailing list