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

Wangshu Jiang wangshu.jiang at icm.uu.se
Wed Nov 1 02:32:48 PDT 2017


Dear Eric,

Thank you very much for such efficient reply and taking my report! The commands work magic and I will have a look at ChimeraX, seem cool and exciting:-)

I am so glad that I actually reach out and ask for support, the problem looks very simple but has hunted me for months.

Thanks again and have a nice day!


Best Regards,

Wangshu

On 01 Nov 2017, at 00:05, Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>> wrote:

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<mailto: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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