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

[Eric Pettersen]

Hi Wangshu,
	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:

bond :42.a at c :43.a at n
bond :47.a at c :48.a at n
bond :51.a at c :52.a at n
bond :125.a at c :126.a at n
bond :47.b at c :48.b at n
bond :48.b at c :49.b at n

	Thanks for reporting the problem.  I will work on a fix.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 31, 2017, at 3:18 PM, Wangshu Jiang <wangshu.jiang at icm.uu.se> wrote:
> 
> 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
> 
> <BrokenPeptide.png>
> Wangshu Jiang
> 
> PhD student
> Dept Cell and Molecular Biology
> BMC Box 596
> Husargatan 3
> 751 24 Uppsala Sweden
> 
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